BIOLOGICAL DIVERSITY: SEED PLANTS

BIOLOGICAL DIVERSITY: SEED PLANTS
Gymnosperms are Seed Plants

Gymnosperms have seeds but not fruits or flowers. Gymnos means naked, sperm means seed: thus the term gymnosperm = naked seeds. Gymnosperms developed during the Paleozoic Era and became the dominant seed plant group during the early Mesozoic Era, as shown in Figure 1. The ancestors of gymnosperms were some now-extinct type of heterosporous fern or related group. There are 700 living species of gymnosperms placed into four divisions: conifers (such as pines and spruce), cycads (such as the sago palm, Cycas revoluta), ginkgos (the maidenhair tree, Ginkgo biloba), and gnetophytes (such as Mormon tea, Ephedra).

Gymnosperms are undoubtedly the group from which the angiosperms developed, although, as Charles Darwin noted in Origin of Species, which group "remains an abominable mystery". Numerous gymnosperm groups have been proposed as flowering plant ancestors over the past century.
Cycads

Cycads are placed in the Division Cycadophyta. They retain several fern-like features, notably pinnate leaves and circinate vernation. However, they usually produce cones of nonphotosynthetic reproductive structures, a distinctively unfernlike feature. Cycads, like all seed plants, are also heterosporous, unlike the ferns which are all homosporous. Cycad cones are unisexual, in fact the plants producing them are dioecious, having separate male and female plants. Cycads also produce free-swimming sperm (a feature found only in ginkgoes among living seed plant groups).

Cycads were much more prominent in the forests of the Mesozoic than they are today. Presently, they are restricted to the tropics. Zamia floridana is the only cycad occurring natively in the continental United States. Several species of Cycas, notably C. revoluta (shown in Figure 2), are commonly encountered cultivated plants in warm, moist areas. Cycas revoluta leaves are often used in Palm Sunday services in some churches, both for their feathery appearance and ease of obtaining from local greenhouses.
Ginkgos

The ginkgoes also were a much more prominent group in the past than they are today. The sole survivor of this once robust and diverse group is Ginkgo biloba, the maidenhair tree shown in Figure 3. Extensively used as an ornamental plant, Ginkgo was thought extinct in the wild until it was discovered growing natively in a remote area of China. Ginkos are dioecious, with separate male and female plants. The males are more commonly planted since the females produce seeds that have a nasty odor. Pollination is by wind. Recently, Ginkgo has become the current herbal rave, although scientific studies have debunked the claim that the herbal supplement made from ginkgoes improves memory. I think.

Precise systematic placement of the ginkgoes has yet to bet determined. Ginkgoes have motile (swimming) sperm, a rarity among living seed plants (only ginkgoes and cycads have this feature today), although the vegetative anatomy of ginkgoes is more conifer-like (long shoot and short shoot morphology discussed below; structure of their wood). Ginkgoes, like the cycads, are dioecious, and also have similar seed features to cycads.

Plants possibly allied to the modern ginkgoes have been found in Permian-aged and later rocks. These plants have been classified in the leaf-genera Ginkgoites (shown in Figure 4) and Baiera, although recent studies suggest these genera are really morphological variants and that the modern genus Ginkgo should be used to include these fossils. During the Mesozoic ginkgoes were worldwide in their distribution and important elements in the gymnosperm forests that dominated the land.
Conifers

The conifers remain a major group of gymnosperms that include the pines, spruce, fir, bald cypress and Norfolk Island Pine (Araucaria). The division Pinophyta contains approximately 550 species of conifers. The conifers are cone producing trees and shrubs that usually have evergreen needle-like leaves. Needles have a thick cuticle, sunken stomates, and a reduced surface area. The conifers, as a group, are well adapted to withstand extremes in climate and occur in nearly all habitats from the equator to the subpolar regions. The taiga biome consists largely of various conifer species.
Auracarias

Members of this group of conifers have numerous small, scale-like leaves spiraling around their stems. Araucaria, a major genus that gives its name to the group, is a common ornamental because of the symmetry and beauty of its growth form. The monkey puzzle tree, shown in Figure 5, is a species of Araucaria.

The fossil record of Auracarias and similar plants is quite good. The fossil genus Auracarioxylon that grew in Arizona during the Triassic Period comprises the largest group of petrified wood in the Petrified Forest National Park of Arizona.
Taxodiaceae: Sequoias and more

Members of this group include some of the largest trees, and have been significant members of the forests of the world since the Mesozoic. Sequoia, shown in Figure 6, and Sequoiadendron are major genera in this group.


The Pine Life Cycle

Pines have an interesting life cycle, shown in Figure 7, that takes two years to complete. Not all seed plants have such a long time span to complete their life history: some flowering plants manage to do it in as little as a few weeks.

The sporophyte, as in all other vascular plant groups, is the dominant, photosynthetic part of the life cycle: when you are holding pine needles in your hand you are holding sporophyte parts. Pines have specialized reproductive structures in which meiosis occurs: pine cones. Pollen grains are produced in the male cones, and contain the male gametophyte (which consists of only a very few cells). Pollen released from the male cones is carried by wind to the female cones, where it lands. The cones close and the next year the pollen grain germinates to produce a pollen tube that grows into the female gametophyte. The sperm cell (from the pollen grain) and egg cell fuse, forming the next generation sporophyte. The sporophyte develops into an embryo encased within a seed. The seed is later released to be transported by the wind to where (hopefully) it lands and germinates. If you have seen a large pine tree you realize there are hundreds or more female cones on such a tree. Pine pollen has been noted to travel great distances from the plant that produced it, if the wind is strong enough. To aid this transport pine pollen has two air sacs, and thus is quite distinctive.

Gnetales |

The Gnetales, are an odd group: they have some angiosperm-like features but are not themselves angiosperms. Cladistic analyses support placement of the gnetales (or some portion of them) as outgroups for the flowering plants. Three distinctive genera comprise this group: Welwitschia, Gnetum, and Ephedra. Ephedra occurs in the western United States where it has the common name "Mormon tea". It is a natural source for the chemical ephedrine, although there is no evidence the Mormons in Utah (where the plant is extremely common) ever used it for tea. Welwitschia is limited to coastal deserts in South Africa, although fossil leaf, cuticle and pollen evidence indicates plants of this type were widespread during the Mesozoic Era. Welwitschia is noted for its two long, prominent leaves. Gnetum has leaves that look remarkably like those in angiosperms, as well as vessels in the xylem, generally considered an angiosperm characteristic.

Among the gnetalean plants, Ephedra is perhaps the best known. One folkloric name for the plant is "Mormon tea". This is a misnomer as there appears little or no evidence that members of a religion that bans stimulants such as caffeine ever brewed a tea from the plant. However, the plant does produce the drug ephedrine, a stimulant lately linked to deaths of athletes.

Welwistchia is a very bizarre plant natively growing only in the coastal deserts of South Africa. The plant produces two long leaves and a crown of reproductive cones rimming a brown, central body. Pollen resembling Welwitschia has been found in many parts of the world, indicating a formerly more widespread distribution of this enigmatic plant.
Angiosperms are Flowering Plants

Flowering plants, the angiosperms, were the last of the seed plant groups to evolve, appearing during the later part of the of the Age of Dinosaurs (the beginning of the Cretaceous, 140 million years ago). All flowering plants produce flowers. Within the female parts of the flower angiosperms produce a diploid zygote and triploid endosperm. Fertilization is accomplished by a variety of pollinators, including wind, animals, and water. Two sperm are released into the female gametophyte: one fuses with the egg to produce the zygote, the other helps form the nutritive tissue known as endosperm.

The angiosperms (angios = hidden) produce modified leaves grouped into flowers that in turn develop fruits and seeds. There are presently 235,000 known living species. Most angiosperms also have larger xylem cells known as vessels that improve the efficiency of their vascular systems.

Whence came the angiosperms? This was Darwin's "abominable mystery". Clearly angiosperms are descended from some group of Mesozoic-aged gymnosperm seed plant....but which one? Click here to view an online lab exercise in phylogeny and try to figure things out!

The classical view of flowering plant evolution suggests early angiosperms were evergreen trees that produced large Magnolia-like flowers. Click here to view an illustration of suggested paths of floral evolution. However, this view has recently been contradicted by the oldest fossil yet found, a 140 million year old plant found by David Dilcher and his associates.

The angiosperms underwent an adaptive radiation during the Cretaceous, and for the most part escaped the major extinctions at the end of the Cretaceous.
Flowers

Flowers are collections of reproductive and sterile tissue arranged in a tight whorled array having very short internodes. Sterile parts of flowers are the sepals and petals. When these are similar in size and shape, they are termed tepals. Reproductive parts of the flower are the stamen (male, collectively termed the androecium) and carpel (often the carpel is referred to as the pistil, the female parts collectively termed the gynoecium). Lily flowers (shown in Figure 10) demonstrates these concepts.

Flowers may be complete, where all parts of the flower are present and functional, or incomplete, where one or more parts of the flower are absent. Many angiosperms produce a single flower on the tip of a shoot (like the lily pictured in Figure 10, or tulips). Other plants produce a stalk bearing numerous flowers, termed an inflorescence, such as is seen in many orchids. Many flowers show adaptations for insect pollination, bearing numerous white or yellow petals. Others, like the grasses, oaks, and elms, are wind pollinated and have their petals reduced and often inconspicuous.
Angiosperm Life Cycle

Flowering plants also exhibit the typical plant alternation of generations, shown in Figure 11. The dominant phase is the sporophyte, with the gametophyte being much reduced in size and wholly dependant on the sporophyte for nutrition. The is not a unique angiosperm condition, but occurs in all seed plants as well. What makes the angiosperms unique is their flowers and the "double fertilization" that occurs. Technically this is not double fertilization, but rather a single egg-sperm fusion (fertilization proper) plus a fusion of the second of two sperm cells with two haploid cells in the female gametophyte to p[produce triploid (3n) endosperm, a nutritive tissue for the developing embryo. More details on this aspect of the flowering plants are available in the FLOWERING PLANT REPRODUCTION: Fertilization and Fruits chapter.
Angiosperm Systematics

The flowering plants, the division Magnoliophyta, contain more than 235,000 species, six times the number of species of all other plants combined. The flowering plants divide into two large groups, informally named the monocots and the dicots. The techjnical names for these groups are the class Magnoliopsida for dicots and the class Liliopsida for monocots.

The dicotyledons are in the class Magnoliopsida and have these features: either woody or herbaceous, flower parts usually in fours and fives, leaves usually net-veined, vascular bundles arranged in a circle within the stem, and produce two cotyledons (seed leaves) at germination. Prominent dicot families include the mustards, maples, cacti, peas and roses. Several dicot families are noteworthy because of the illegal drugs (shown in Figure 12) derived from them: the Cannabinaceae (marijuana) and Papaveraceae (poppies from which opium and heroin are derived). Erythroxylum coca (in the dicot family Erythroxylaceae) is the plant from which the illegal drug cocaine is extracted.

Not all dicot plants are misused to produce illegal drugs. Notable dicot families with legitimate uses include the pea family, which includes the crop plants beans, clover, and peas as well as many ornamental landscape plants such as Acacias. Beans are an excellent source of nonanimal protein as well as fiber. Another dicot of enormous use is cotton, Gossypium, shown in Figure 13. Chocolate and cola are products of the plant family Sterculiaceae. Coffee is produced from Coffea arabica, a plant in the family Rubiaceae, while tea comes from Camelia sinensis (Theaceae), a plant native to China.

The class Liliopsida has plants that are herbaceous (a majority are, only palms and bamboo stand out as monocot trees), flower parts are in threes, leaves are usually parallel-veined, vascular bundles are scattered within the stem, and produce one cotyledon (seed leaf) at germination. Monocot families include lilies, palms, orchids, irises, and grasses.

The monocot family Poaceae (known previously as the Gramineae) includes the grasses such as corn, oats, wheat, rye, and rice that are staple food products as well as ornamental plants such as crabgrass and tiff grass. The importance of this plant family to modern civilization cannot be overstated, as the first six plants mentioned in the previous sentence provide 75% of our food, either directly as food we eat or indirectly as food for animals we eat.
Trends in Plant Evolution

Several evolutionary trends within the plant kingdom have been noted. The monophyletic nateure of this kingdom is not in dispute, with the first major division being between vascular and nonvascular plants. Wihin the vascular plants we see increasing changes in the relationship between sporophyte and gametophyte, culminating in flowering plants.

Developing from green algal ancestors, plants show a trend for reduction of the complexity, size, and dominance of the gametophyte generation. In nonvascular plants the gametophyte is the conspicuous, photosynthetic, free-living phase of the life cycle. Conversely, the angiosperm gametophyte is reduced to between three and eight cells (hence it is very inconspicuous) and is dependent on the free-living, photosynthetic sporophyte for its nutrition.

Plants also developed and refined the root-shoot-leaf axis with its specialized conducting cells of the xylem and phloem. The earliest vascular plants, such as Cooksonia and Rhynia, were little more than naked (unleafed) photosynthetic stems. Some plants later developed secondary growth that produced wood. Numerous leaf modifications are known, including "carnivorous" plants such as the Venus flytrap, as well as plants that have reduced or lost leaves, such as Psilotum and the cacti.

A third trend is the development of the seed to promote the dormancy of the embryo. The seed allows the plant to wait out harsh environmental conditions. With the development of the seed during the Paleozoic era plants became less prone to mass extinctions.

The fourth trend in plant evolution is the encasing of a seed within a fruit. The only plant group that produces true fruit is the flowering plants, the angiosperms. Fruits serve to protect the seed, as well as aid in seed dispersal.

All text contents ©1995, 1999, 2000, 2001, 2003, 2004, by M.J. Farabee. Use of text for educational purposes is encouraged.

Email: nolvyhindarto@gmail.com

BIOLOGICAL DIVERSITY: NONVASCULAR PLANTS AND NONSEED VASCULAR PLANTS

BIOLOGICAL DIVERSITY: NONVASCULAR PLANTS AND NONSEED VASCULAR PLANTS

The plant kingdom contains multicellular phototrophs that usually live on land. The earliest plant fossils are from terrestrial deposits, although some plants have since returned to the water. All plant cells have a cell wall containing the carbohydrate cellulose, and often have plastids in their cytoplasm. The plant life cycle has an alternation between haploid (gametophyte) and diploid (sporophyte) generations. There are more than 300,000 living species of plants known, as well as an extensive fossil record.

Plants divide into two groups: plants lacking lignin-impregnated conducting cells (the nonvascular plants) and those containing lignin-impregnated conducting cells (the vascular plants). Living groups of nonvascular plants include the bryophytes: liverworts, hornworts, and mosses. Vascular plants are the more common plants like pines, ferns, corn, and oaks. The phylogenetic relationships within the plant kingdom are shown in Figure 1.
Evolution of Plants

Fossil and biochemical evidence indicates plants are descended from multicellular green algae. Various green algal groups have been proposed for this ancestral type, with the Charophytes often being prominently mentioned. Cladistic studies support the inclusion of the Charophytes (including the taxonomic order Coleochaetales) as sister taxa to the land plants. Algae dominated the oceans of the precambrian time over 700 million years ago. Between 500 and 400 million years ago, some algae made the transition to land, becoming plants by developing a series of adaptations to help them survive out of the water.

Vascular plants appeared by 350 million years ago, with forests soon following by 300 million years ago. Seed plants next evolved, with flowering plants appearing around 140 million years ago
The Plant Life Cycle

Plants have an alternation of generations: the diploid spore-producing plant (sporophyte) alternates with the haploid gamete-producing plant (gametophyte), as shown in Figure 3. Animal life cycles have meiosis followed immediately by gametogenesis. Gametes are produced directly by meiosis. Male gametes are sperm. Female gametes are eggs or ova.

The plant life cycle has mitosis occurring in spores, produced by meiosis, that germinate into the gametophyte phase. Gametophyte size ranges from three cells (in pollen) to several million (in a "lower plant" such as moss). Alternation of generations occurs in plants, where the sporophyte phase is succeeded by the gametophyte phase. The sporophyte phase produces spores by meiosis within a sporangium. The gametophyte phase produces gametes by mitosis within an antheridium (producing sperm) and/or archegonium (producing eggs). These different stages of the flowering plant life cycle are shown in Figure 4. Within the plant kingdom the dominance of phases varies. Nonvascular plants, the mosses and liverworts, have the gametophyte phase dominant. Vascular plants show a progression of increasing sporophyte dominance from the ferns and "fern allies" to angiosperms.
Homospory and Heterospory

Plants have two further variations on their life cycles. Plants that produce bisexual gametophytes have those gametophytes germinate from isospores (iso=same) that are about all the same size. This state is referred to as homospory (sometimes referred to as isospory). A generalized homosporous plant life cycle is shown in Figure 5. Homosporous plants produce bisexual gametophytes. Ferns are a classic example of a homosporous plant.

Plants that produce separate male and female gametophytes have those gametophytes germinate from (or within in the case of the more advanced plants) spores of different sizes (heterospores; hetero=different). The male gametophyte produces sperm, and is associated with smaller or microspores. The female gametophyte is associated with the larger or megaspores. Heterospory is considered by botanists as a significant step toward the development of the seed. A generalized heterosporous life cycle is shown in Figure 6.
Plant Adaptations to Life on Land

Organisms in water do not face many of the challenges that terrestrial creatures do. Water supports the organism, the moist surface of the creature is a superb surface for gas exchange, etc. For organisms to exist on land, a variety of challenges must be met.

1. Drying out. Once removed from water and exposed to air, organisms must deal with the need to conserve water. A number of approaches have developed, such as the development of waterproof skin (in animals), living in very moist environments (amphibians, bryophytes), and production of a waterproof surface (the cuticle in plants, cork layers and bark in woody trees).
2. Gas exchange. Organisms that live in water are often able to exchange carbon dioxide and oxygen gases through their surfaces. These exchange surfaces are moist, thin layers across which diffusion can occur. Organismal response to the challenge of drying out tends to make these surfaces thicker, waterproof, and to retard gas exchange. Consequently, another method of gas exchange must be modified or developed. Many fish already had gills and swim bladders, so when some of them began moving between ponds, the swim bladder (a gas retention structure helping buoyancy in the fish) began to act as a gas exchange surface, ultimately evolving into the terrestrial lung. Many arthropods had gills or other internal respiratory surfaces that were modified to facilitate gas exchange on land. Plants are thought to share common ancestry with algae. The plant solution to gas exchange is a new structure, the guard cells that flank openings (stomata) in the above ground parts of the plant. By opening these guard cells the plant is able to allow gas exchange by diffusion through the open stomata.
3. Support. Organisms living in water are supported by the dense liquid they live in. Once on land, the organisms had to deal with the less dense air, which could not support their weight. Adaptations to this include animal skeletons and specialized plant cells/tissues that support the plant.
4. Conduction. Single celled organisms only have tyo move materials in, out, and within their cells. A multicellular creature must do this at each cell in the body, plus move material in, out, and within the organism. Adaptations to this include the circulatory systems of animals, and the specialized conducting tissues xylem and phloem in plants. Some multicellular algae and bryophytes also have specialized conducting cells.
5. Reproduction. Organisms in water can release their gametes into the water, where the gametes will swim by flagella until they ecounter each other and fertilization happens. On land, such a scenario is not possible. Land animals have had to develop specialized reproductive systems involving fertilization when they return to water (amphibians), or internal fertilization and an amniotic egg (reptiles, birds, and mammals). Insects developed similar mechanisms. Plants have also had to deal with this, either by living in moist environments like the ferns and bryophytes do, or by developing specialized delivery systems like pollen tubes to get the sperm cells to the egg.

Bryophytes

Bryophytes are small, nonvascular plants that first evolved approximately 500 million years ago. The earliest land plants were most likely bryophytes. Bryophytes lack vascular tissue and have life cycles dominated by the gametophyte phase, as shown in Figure 7. The lack of conducting cells limits the size of the plants, generally keeping them under 5 inches high. Roots are absent in bryophytes, instead there are root-like structures known as rhizoids. Bryophytes include the hornworts, liverworts, and mosses.
Tracheophytes: The Vascular Plants

The vascular plants have specialized transporting cells xylem (for transporting water and mineral nutrients) and phloem (for transporting sugars from leaves to the rest of the plant). When we think of plants we invariably picture vascular plants. Vascular plants tend to be larger and more complex than bryophytes, and have a life cycle where the sporophyte is more prominent than the gametophyte. Vascular plants also demonstrate increased levels of organization by having organs and organ systems. The novel features oif the vascular plants are summarized in Table 2.
Vascular Plant Groups

Vascular plants first developed during the Silurian Period, about 400 million years ago. The earliest vascular plants had no roots, leaves, fruits, or flowers, and reproduced by producing spores.

Cooksonia, shown in Figure 8, is a typical early vascular plant. It was less than 15 cm tall, with stems that dichotomously branched. Dichotomous branching (where the stem divides into two ewqual branches) appears a primitive or ancestral trait in vascular plants. Some branches terminated in sporangia that produced a single size of spore.

Many scientists now consider "Cooksonia" an evolutionary grade rather than a true monophyletic taxon. Their main argument is that not all stems of Cooksonia-type plants have vascular tissue. The evolutionary situation of a grade would have some members of the group having the trait, others not. The shapes of sporangia on various specimens of Cooksonia also vary considerably.

Rhynia, shown in Figure 9, is another early vascular plant. Like Cooksonia, it lacked leaves and roots. One of the species formerly assigned to this genus, R. major, has since been reclassified as Aglaophyton major. Some paleobotanists consider A. major (Figure 10) a bryophyte, however, it does have a separate free-living sporophyte that is more prominent than the sporophyte, but appears to lack lignified conducting cells. The remaining species, R. gwynne-vaughanii is an undoubted vascular plant.

Devonian plant lines included the trimerophytes and zosterophyllophytes, which have been interpreted as related to ferns and lycophytes.
The Psilophytes

The Division Psilophyta consists of Psilotum nudum (the whisk fern, shown in Figure 11), a living plant that resembling what paleobotanists believe Cooksonia to have been: a naked, photosynthetic stem bearing sporangia. Also in the group is Tmesipteris, which resembles Psilotum except for its possession of smallo vascularized leaves arising on opposite sides of the stem. However, most paleobotanists doubt that Psilotum is a direct descendant of Cooksonia. Molecular studies suggest an affiliation with ferns for Psilotum. Psilotum also has three fused sporangia, termed a synangium, located on the sides of the stems (instead of the tips of stems as in Cooksonia).
The Lycophytes

The next group, the Division Lycophyta, have their sporangia organized into strobili (singular: strobilus). A strobilus is a series of sporangia and modified leaves closely grouped on a stem tip. The leaves in strobili are soft and fleshy as opposed to the hard, modified leaves in cones.

Leaves that contained vascular tissue are another major advance for this group. The presumed evolutionary pathway for the leaf is shown in Figure 12. The leaves in lycophytes, both living and fossil forms, are known as microphylls. This term does not imply any size constraint, but rather refers to the absence of a leaf gap in the vascular supply of the stem at the point where the leaf vascular trace departs. Ferns and other plants have megaphylls, leaves that produce this leaf gap.

Today there are fewer genera of lycophytes than during the group's heyday, the Paleozoic Era. Major living lycophytes include Lycopodium (commonly called the club moss [shown in Figure 13], although it is NOT a moss), Isoetes, and Selaginella (the so-called resurrection plant). Lycopodium produces isospores that germinate in the soil and produce a bisexual gametophyte. These spores are all approximately the same size. Selaginella and Isoetes are heterosporous, and thus produce two sizes of spores: small spores (termed microspores) that germinate to produce the male gametophyte; and larger spores (megaspores) that germinate to produce the female gametophyte. The production of two sizes of spores, and also making separate unisexual gametophytes, is thought an important step toward the seed. Modern lycophytes are small, herbaceous plants. Many of the prominent fossil members of this group produced large amounts of wood and were significant trees in the Carboniferous-aged coal swamps.

Selaginella is a heterosporous member of the lycophytes. Some species of this genus are able to withstand drying out by going dormant until they are rehydrated. For this reason these forms of the genus are commonly called resurrection plants. An example of this is shown in Figure 14.
Fossil Lycophytes: Baragwanathia and Drepanophycus

Baragwanathia, shown in Figure 15, is an undoubted lycophyte from the middle Silurian deposits of Australia. It has microphyllous leaves spirally attached to the stem, and sporangia clustered in some areas of the plant, although not in terminal strobili as in modern lycophytes.

Drepanophycus is a middle Devonian lycophyte from the Northern Hemisphere, also shown in Figure 15. Its features are very similar to modern lycophytes.
Lepidodendron and Sigillaria

The Lycophytes became significant elements of the world's flora during the Carboniferous time (the Mississippian and Pennsylvanian are terms used for this time span in the United States). These non-seed plants evolved into trees placed in the fossil genera Lepidodendron and Sigillaria, with heights reaching up to 40 meters and 20-30 meters respectively. Lepidodendron stems are composed of less wood (secondary xylem) that usually is found in gymnosperm and angiosperm trees.

We know much about the anatomy of these coal-age lycopods because of an odd type of preservation known as a coal ball. Coal balls can be peeled and the plants that are anatomically preserved within them laboriously studied to learn the details of cell structure of these coal age plants. Additionally, we have some exceptional petrifactions and compressions that reveal different layers of the plants' structure. Estimates place the bulk, up to 70%, of coal material as being derived from lycophytes.

Lepidodendron, pictured in Figures 16 and 17, was a heterosporous lycophyte tree common in coal swamps of the Carboniferous time. As with many large plant fossils, one rarely if ever finds the entire tree preserved intact. Consequently there are a number of fossil plant genera that are "organ taxa" and represent only the leaves (such as Lepidophylloides), reproductive structures (Lepidostrobus), stem (Lepidodendron), spores (Lycospora), and roots (Stigmaria). Lepidodendron had leaves borne spirally on branches that dichotomously forked, with roots also arising spirally from the stigmarian axes, and both small (microspores) and large (megaspores) formed in strobili (a loose type of soft cone). Lepidodendron may have attained heigths of nearly 40 meters, with trunks nearly 2 meters in diameter. The trees branched extensively and produced a large number of leaves. When these leaves fell from the branches, they left behind them the leaf scars characteristic of the genus.

Sigillaria was another arborescent lycopod, and is also common in coal-age deposits. In contrast to the spirally borne leaves of Lepidodendron, Sigillaria had leaved arranged in vertical rows along the stem.
The Sphenophyta

The Division Sphenophyta contains once dominant plants (both arborescent as well as herbaceous) in Paleozoic forests, equisetophytes are today relegated to minor roles as herbaceous plants. Today only a single genus, Equisetum, survives. The group is defined by their jointed stems, with many leaves being produced at a node, production of isospores in cones borne at the tips of stems, and spores bearing elaters (devices to aid in spore dispersal). Sporophyte features are seen in Figure 18. The gametophyte is small, bisexual, photosynthetic, and free-living. Silica concentrated in the stems give this group one of their common names: scouring rushes. These plants were reportedly used by American pioneers to scour the pots and pans. The fossil members of this group are often encountered in coal deposits of Carboniferous age in North America and Europe.
The Ferns

Ferns reproduce by spores from which the free-living bisexual gametophyte generation develops. There are 12,000 species of ferns today, placed in the Division Pteridophyta. The fossil history of ferns shows them to have been a dominant plant group during the Paleozoic Era. Most ferns have pinnate leaves, exhibiting small leaflets on a frond, as shown in Figure 19. Ferns have megaphyllous leaves, which cause a leaf gap in the vascular cylinder of the stem/rhizome, as shown in Figure 20. The first ferns also appear by the end of the Devonian. Some anatomical similarities suggest that ferns and sphenophytes may have shared a common ancestor within the trimerophytes.
The Fern Life Cycle

The fern gametophyte has both sexes present and is referred to as a prothallium. Prothallia develop from spores shed from the underside of the sporophyte leaves, Once fertilization occurs, the next generation sporophyte develops from the egg located in the prothallium.

Composite of 4 segmented diagrams of the fern life cycle. Note: to view this in its proper sequence you will need to open your browsert window as wide as possible. Images from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.



All text contents ©1995, 1999, 2000, 2001, 2003, 2004, by M.J. Farabee. Use of the text for educational purposes is encouraged.

Email: nolvyhindarto@gmail.com

BIOLOGICAL DIVERSITY: CLASSIFICATION

Biological Diversity and Classification

Taxonomy is that branch of biology dealing with the identification and naming of organisms. The ancient Greek philosopher Aristotle apparently began the discussion on taxonomy. British naturalist John Ray is credited with revising the concept of naming and describing organisms. During the 1700s, Swedish botanist Carolus Linneus classified all then-known organisms into two large groups: the kingdoms Plantae and Animalia. Robert Whittaker in 1969 proposed five kingdoms: Plantae, Animalia, Fungi, Protista, and Monera. Other schemes involving an even greater number of kingdoms have lately been proposed, however most biologists employ Whittaker's five kingdoms. Recent studies suggest that three domains be employed: Archaea, Bacteria, and Eukarya.

Linneus attempted to pigeon-hole (or classify) all known species of his time (1753). Linnean hierarchical classification was based on the premise that the species was the smallest unit, and that each species (or taxon) nested within a higher category.

Linneus also developed the concept of binomial nomenclature, whereby scientists speaking and writing different languages could communicate clearly. For example Man in English is Hombre in Spanish, Herr in German, Ren in Chinese, and Homo in Latin. Linneus settled on Latin, which was the language of learned men at that time. If a scientist refers today to Homo, all scientists know what organism/taxon he or she means.
Construction of Phylogenetic Trees

Taxonomy is part of a larger division of biology known as systematics. Determination of phylogeny is a goal of systematics. This is done by the construction of phylogenetic trees, which in a sense represent evolutionary hypotheses and attempts to define monophyletic groups. To build these trees, we must have data, which comes from the characteristics used in classification. There are several methods of classification: traditional, phentic, and cladistic. They differ in how they value certain characters.
Traditional Classification

Data used in traditional systematics stresses both common ancestry (monophylesis) and the amount of divergence among groups. The traditional, dating to Linneaus view, is that birds have feathers, reptiles have scales, and mammals have hair. Using this as a major character, a classification like that above has been constructed. Fossils, evidence of past life, are not included in this classification. Since all of these groups have the amniotic egg, or a modification of it, they would be united in a larger taxon. Linneus placed each of these groups in a separate class within the Phylum Chordata. A primitive character is one present in the common ancestor and all members of the group, such as the amniotic egg. A derived character is one found only in a particular lineage within the larger group. In our example above, hair and feathers may be viewed as derived characters. A traditional view of our example group is that birds and mammals evolved from reptiles due to their unique derived characters.
Cladistics and Cladograms

Cladistics is a type of systematics developed by the late German biologist Willi Hennig, who attempted to formulate a more objective method of classifying organisms. Cladists group organisms based on the presence of shared derived characters, not the overall similarity of potential group members. In the example cited in Figure 3, the amniotic egg would be used to unite a group sharing common ancestry, since it would NOT be present in a group that was not in the lineage. The use of feathers and hair to separate birds and mammals from reptiles would NOT factor into a cladistic hypothesis, or cladogram, since these are characters unique to only one taxon in our group.

The value of cladistics lies in its capacity to generate (and provide a set of criteria for the evaluation) of multiple hypotheses (alternate cladograms) that can be evaluated with additional data. Almost always the "correct" cladogram employs the principle of parsimony, which proposes that the shortest number of steps or character state changes is most likely correct. An important question....is evolution always parsimonmious? However the ultimate answer to that question unfolds, the rigor cladistics introduces to systematics is useful in getting traditional systematists to look at their subjective classifications in a new light. On the diagram shown in Figure 5, shared derived characters are indicated as hauchers across the lines. The mammal clade (in this case represented by mouse and chimpanzee) is united by fur, the lizard, pigeon, mouse-chimp clade is united by claws or nails, etc.
Cladistic Classification

The example used above, if treated cladistically, would produce a very different classification! Note that crocodiles have more in common (in a cladistic sense) with birds than they do with other reptiles. Birds and crocs form a clade, or monophyletic group united by shared derived characters not present in the other groups. If we construct a Linnean group from this cladogram, we have a class of birds and crocodiles, a second class of lizards, snakes, and turtles, and a third class of mammals,

One of the more interesting applications of cladistics is to the question of the pandas. The giant panda was once thought to be a bear, but later its racoon-like characters caused it to be placed closer to racoons. The red (lesser) panda lives in the same areas of China as the giant panda, but has a far greater similarity with racoons,. DNA hybridization studies suggest the giant panda is in the bear clade, while the red panda is in the racoon clade. Both share a common ancestry, as indicated by shared derived characters, followed by convergent evolution of other characters. The diagram above indicates this divergence from common ancestry, and even attempts to show the time of that divergence.
Phenetics

Phenetics is a process by which taxa are clustered together based on the number of their similarities (or differences, depending on the numerical coefficient employed). Traits are measured and either converted into integers or input directly as numerical data. Theses data are then mathematically processed using an algorithm that generates a similarity (or distance as the case may be) matrix. Various graphical representations of this matrix include a phenogram, and principal coordinate plot. Phenetic classifications are plagued by problems of convergence and parallelism, but are useful in their attempt to objectify the classification process. My previous work on triprojectate pollen employed phenetics to deal with a wide array of subjective ratios or other classification methods. Convergence was a given with this group of fossil pollen produced by one or more groups of unknown extinct plants. Since monophylesis could not be established for the entire group, phenetics was use to help delineate possible monophyletic groups for eventual cladistic study.
Nomenclature

The naming of species and other taxa follows a set of rules, the International Code of Botanical Nomenclature for plants, the International Code of Zoological Nomenclature (ICZN) for animals.

Some general rules for nomenclature:

1. All taxa must belong to a higher taxonomic group. Often a newly discovered organism is the sole species in a single genus, within a single family...etc.
2. The first name to be validly and effectively published has priority. This rule has caused numerous name changes, especially with fossil organisms: Brontosaurus is invalid, and the correct name for the big sauropod dinosaur is Apatosaurus, Eohippus (the tiny "dawn horse") is invalid and should be referred to as Hyracotherium. Sometime, however, names can be conserved if a group of systematists agrees.
3. All taxa must have an author. When you see a scientific name such as Homo sapiens L, the L stands for Linneus, who first described and named that organism. Most scientists must have their names spelled out, for example Libopollis jarzenii Farabee et al. (an interesting fossil pollen type I stumbled across a very long time ago!).

The Kingdoms of Life

Linnaeus originally placed all living things into either the plant or animal kingdoms. As scientists learned more about the biology of many organisms, this constraining into two kingdoms became less and less defensible.

Evolutionary theory and the cell theory provide us with a basis for the interrelation of all living things. We also utilize Linneus' hierarchical classification system, adopting (generally) five kingdoms of living organisms. Viruses, as discussed later, are not considered living. Recent studies suggest that there might be a sixth Kingdom, the Archaea.

Monera

Monera are the only kingdom composed of prokaryotic organisms, they have a cell wall, and lack both membrane-bound organelles and multicellular forms. The Archaebacteria, the most ancient of this kingdom, are so different that they may belong to a separate kingdom. Other groups of Monera include the cyanobacteria (autotrophic) and eubacteria (heterotrophic).

Protista

The most ancient eukaryotic kingdom, protists include a variety of eukaryotic body (single-celled-colonial-multicellular?) and nutritional heterotrophic, autotrophic, and both) forms. Perhaps they are best defined as eukaryotes that are NOT fungi, animals, or plants.

Fungi

Fungi are a eukaryotic, heterotrophic, usually multicellular group having multinucleated cells enclosed in cells with cell walls. They obtain their energy by decomposing dead and dying organisms and absorbing their nutrients from those organisms. Some fungi also cause disease (yeast infections, rusts, and smuts), while others are useful in baking, brewing, as foods, drugs and sources for antibiotics.

Plantae

Plants are immobile, multicellular eukaryotes that produce their food by photosynthesis and have cells encased in cellulose cell walls. Plants are important sources of oxygen, food, and clothing/construction materials, as well as pigments, spices, dyes, and drugs.

Animalia

* Animals are multicellular, heterotrophic eukaryotes that are capable of mobility at some stage during their lives, and that have cells lacking cell walls. Animals provide food,

Text ©1998, 2000, 2001, 2002, by M.J. Farabee, all rights reserved. Use for educational purposes is encouraged.

Email: nolvyhindarto@gmail.com

ATP AND BIOLOGICAL ENERGY

The Nature of ATP

Adenosine triphosphate (ATP), the energy currency or coin of the cell pictured in Figfures 1 and 2, transfers energy from chemical bonds to endergonic (energy absorbing) reactions within the cell. Structurally, ATP consists of the adenine nucleotide (ribose sugar, adenine base, and phosphate group, PO4-2) plus two other phosphate groups.

Energy is stored in the covalent bonds between phosphates, with the greatest amount of energy (approximately 7 kcal/mole) in the bond between the second and third phosphate groups. This covalent bond is known as a pyrophosphate bond.

We can write the chemical reaction for the formation of ATP as:

a) in chemicalese: ADP + Pi + energy ----> ATP

b) in English: Adenosine diphosphate + inorganic Phosphate + energy produces Adenosine Triphosphate

The chemical formula for the expenditure/release of ATP energy can be written as:

a) in chemicalese: ATP ----> ADP + energy + Pi

b) in English Adenosine Triphosphate produces Adenosine diphosphate + energy + inorganic Phosphate

An analogy between ATP and rechargeable batteries is appropriate. The batteries are used, giving up their potential energy until it has all been converted into kinetic energy and heat/unusable energy. Recharged batteries (into which energy has been put) can be used only after the input of additional energy. Thus, ATP is the higher energy form (the recharged battery) while ADP is the lower energy form (the used battery). When the terminal (third) phosphate is cut loose, ATP becomes ADP (Adenosine diphosphate; di= two), and the stored energy is released for some biological process to utilize. The input of additional energy (plus a phosphate group) "recharges" ADP into ATP (as in my analogy the spent batteries are recharged by the input of additional energy).
How to Make ATP

Two processes convert ADP into ATP: 1) substrate-level phosphorylation; and 2) chemiosmosis. Substrate-level phosphorylation occurs in the cytoplasm when an enzyme attaches a third phosphate to the ADP (both ADP and the phosphates are the substrates on which the enzyme acts). This is illustrated in Figure 3.

Enzymes in chemiosmotic synthesis are arranged in an electron transport chain that is embedded in a membrane. In eukaryotes this membrane is in either the chloroplast or mitochondrion. According to the chemiosmosis hypothesis proposed by Peter Mitchell in 1961, a special ATP-synthesizing enzyme is also located in the membranes. Mitchell would later win the Nobel Prize for his work.

During chemiosmosis in eukaryotes, H+ ions are pumped across an organelle membrane by membrane "pump proteins" into a confined space (bounded by membranes) that contains numerous hydrogen ions. This is shown in Figure 4 and 5. The energy for the pumping comes from the coupled oxidation-reduction reactions in the electron transport chain. Electrons are passed from one membrane-bound enzyme to another, losing some energy with each tansfer (as per the second law of thermodynamics). This "lost" energy allows for the pumping of hydrogen ions against the concentration gradient (there are fewer hydrogen ions outside the confined space than there are inside the confined space). The confined hydrogens cannot pass back through the membrane. Their only exit is through the ATP synthesizing enzyme that is located in the confining membrane. As the hydrogen passes through the ATP synthesizing enzyme, energy from the enzyme is used to attach a third phosphate to ADP, converting it to ATP.

Usually the terminal phosphate is not simply removed, but instead is attached to another molecule. This process is known as phosphorylation.

W + ATP -----> W~P + ADP where W is any compound, for example:

glucose + ATP -----> glucose~P + ADP

Glucose can be converted into Glucose-6-phosphate by the addition of the phosphate group from ATP.

ATP serves as the biological energy company, releasing energy for both anabolic and catabolic processes and being recharged by energy generated from other catabolic reactions.