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6:06 AM
The Chrysophyceae, classified within the kingdom Chromista, are mostly unicellular or colonial organisms found in fresh and salt water throughout the world.

The Chrysophyceae (in some systems corresponding to the phylum Chrysophyta) are related to heterokont algae and include more than eight hundred described species that are classified in approximately one hundred genera.

They aremost closely related to the Synurophyceae and other pigmented heterokont algae, including the Bacillariophyceae (diatoms), Eustigmatophyceae, Phaeophyceae (brown algae), and Xanthophyceae (yellow-green algae), among others.

The classification of chrysophycean species remains in a state of flux. In one system of classification primary importance is placed upon the number of flagella (zero, one, or two) that are present in the motile cell stage.


A second classification organizes species based upon the predominant vegetative state of the organism. For example, in this classification amoeboid, coccoid, palmelloid, and flagellate species are assigned to separate orders.

Ecology and Diversity

Chrysophytes are predominantly found in fresh-water environments, although some are marine, and a few are reported from soil or snow.

Members of the group are widely distributed but are most common in cold-temperate lakes, ponds, bogs, and ditches. Some species are common members of the phytoplankton,whereas others are epibionts or are neustonic (attached to the surface film of quiet water). Other species are only rarely observed.

Most chrysophytes are free-swimming unicellular or colonial flagellates. Others are coccoid (that is, immobile, walled unicells), amoeboid, or palmelloid (with cells enveloped in a gelatinous matrix). A few species are parenchymatous.

Cell Walls

Most chrysophytes lack a cell wall, but others produce species-specific outer coverings of scales or loricae. For example, complex siliceous scales or spines that are produced in silica deposition vesicles cover the cells of Paraphysomonas. The scales of Chrysolepidomonas are organic and of two types: those that are dendritic (tree-shaped) and those that are canistrate (cylindrical).

The cells of other species may be enclosed within an organic vaselike or flasklike lorica composed of cellulose and proteins or chitin (for example, Dinobryon, Pseudokephyrion, Poteriochromonas, Lagynion, and Stenocalyx).

In such species the lorica is typically composed of fine, interwoven fibrils. In Dinobryon these fibrils are helically arranged and secreted as the cell rotates about its longitudinal axis.

In contrast, the loricae of Epipyxis species are composed of imbricate, overlapping scales. The posterior pole of the cell is typically positioned at the base of the lorica and may be attached by a fine cytoplasmic extension; the flagella protrude externally through the lorica opening.

Flagella

Chrysophytes are heterokont, biflagellate organisms that swim with at least one flagellum forwardly directed. The two flagella ofmotile cells are anteriorly inserted in an apical or subapical position and are unequal in length.

The flagella differ morphologically and are heterodynamic. In most species, the basal bodies from which the flagella arise are either oriented at an acute angle to one another or are perpendicular to one another.

In Hydrurus, Chromphyton, and Lagynion, the basal bodies form an obtuse (oblique) angle with respect to one another. The long (immature) flagellum is anteriorly directed and is ornamented with two rows ofmastigonemes and finer lateral filaments. Eachmastigoneme is composed of a base, a tubular shaft, and one to three terminal filaments; these are known as tripartite tubular hairs.

Mastigonemes are produced in the perinuclear space between the two outer membranes of the chloroplast and the two surrounding membranes of the chloroplast endoplasmic reticulum. The long flagellum beats in an undulatory, sine-wave-like motions that are initiated at the base of the flagellum.

The relatively stiff short (mature) flagellum is directed laterally or posteriorly, lacks mastigonemes, and rotates helically. A distinct swelling associated with the eyespot is typically present at the proximal base of the smooth flagellum.

In some taxa (such as Chromulina, Chrysococcus, and Sphaleromantis), the short flagellum is highly reduced and may be nonemergent; it is therefore undetectable by light microscopy. In a handful of species the short flagellum is entirely absent, although the mature basal body may persist within the cell.

Naked motile cells bearing two visible flagella are often referred to as Ochromonas-like (or ochromonadalean), whereas those with one visible flagellum are typically assigned to the genus Chromulina.

The transitional region between the basal body and flagellum contains an electron-dense transitional plate, above which lies a coiled, apparently springlike transitional helix. The functions of the transitional plate and helix, which are also found in other flagellates, are uncertain.

In heterotrophic and mixotrophic species, the flagella play a role in prey capture. Particles actively captured by the flagella that are recognized as food are pushed into a feeding basket; those not recognized as food are released.

The feeding basket is formed and closed by movements of underlying microtubules. Water currents produced by the undulation of the long flagellum may passively bring food particles in contact with the cells that, in some species, are collected by pseudopodia.

Cell Organization

Cells possess a single pear-shaped nucleus that is positioned at the anterior end of the cell. The narrow end of the nucleus typically lies close to the basal bodies. A prominent Golgi apparatus with distended cisternae lies against the nucleus. Contractile vacuoles (absent in some marine forms) are also found at the anterior end of the cell.

One or more mitochondria with tubular cristae are present in the cell. Because the mitochondria are usually long and coiled, the actual number of mitochondria present is difficult to discern. Fibrous bands, sometimes referred to as connecting fibers, connect the basal bodies to one another.

A cross-striated band of fibers known as the rhizoplast extends from the basal apparatus and forms a connection to the nucleus. Typically four microtubular roots (R1, R2, R3, and R4) originate near the basal bodies, take characteristic paths through the cell, and proliferate beneath the plasmalemma.

For example, in most species roots R3 and R4 often form a loop beneath the short flagellum. Other microtubules are nucleated from the four major roots that provide the cytoskeletal elements needed to maintain cell shape.

Muciferous bodies or discobolocysts are present in some species. Muciferous bodies are capable of extruding long threads, whereas discobolocysts forcefully eject discoid projectiles. These functions of these organelles have been little studied but may be involvedin prey capture or predator avoidance.

Nutrition

The Chrysophyceae employ a variety of means to obtain energy. Most chrysophytes are photosynthetic but require an exogenous source of vitamins (such as vitamin B12, biotin, and thiamin) for growth.

It is probable that all chrysophytes are opportunistically or facultatively osmotrophic; that is, they are capable of directly absorbing small inorganic or organic molecules (such as sugars and amino acids) from the surrounding medium. Several species, particularly those with leucoplasts, are obligate heterotrophs that are bactivorous or consume small organic particles.

Mixotrophic species are also well represented among the chrysophytes. This category includes photosynthetic species that, routinely or under unfavorable conditions, supplement their nutrition via phagotrophy.

Chloroplasts, Photosynthetic Pigments, and Storage Products

The chloroplasts of chrysophytes are typically golden-brown or yellow-green in color, and there are usually one to two chloroplasts per cell.

Chloroplasts are peripherally located, and pyrenoids may be present or absent. Four unit membranes surround each chloroplast; the outer two are derived from the endoplasmic reticulum and are typically continuous with the nuclear envelope.

Chloroplast lamellae are typically composed of three adpressed thylakoid membranes, and a girdle lamella, which completely encircles the chloroplast, is usually present. The chloroplast deoxyribonucleic acid (DNA) is ring-shapedandlies just beneath the girdle lamella.

The light-harvesting complex of chrysophytes contains chlorophylls a and c, beta-carotene, and the xanthophylls fucoxanthin, neoxanthin, violaxanthin, and zeaxanthin. Among these, fucoxanthin is dominant and is therefore responsible for the golden-brown color observed in most chrysophytes.

The major product of photosynthesis is a water-soluble ο-1,3-linked glucan (known as chrysolaminarin or leucosin) that is stored in cytoplasmic vacuoles in the posterior region of the cell. Lipids may also be produced and are also stored in the cytoplasm.

Eyespots (or stigmata) are present in many, but not all, species. The eyespot takes the form of a single layer of orange or reddish colored, lipidlike droplets that are located just beneath the chloroplast membrane. These droplets lie near a swelling located at the base of the smooth (short) flagellum; together the eyespot and flagellar swelling form a photoreceptor apparatus.

Several chrysophyte genera are known that contain a vestigial chloroplast (leucoplast) that lacks pigments (including Anthophysa, Monas, Oikomonas, Paraphysomonas, and Spumella).

Reproduction

Asexual reproduction in amoeboid and flagellate species occurs by longitudinal division of the cell; fragmentation is common among colonial, palmelloid, and parenchymatous species. In coccoid species reproduction may proceed via cell division or the formation of autospores that rupture and exit the parent cell wall.

Some taxa, such as the parenchymatous genera Phaeodermatium and Hydrurus or members of the palmelloid family Chrysocapsaceae, reproduce by means of flagellated swarmers (zoospores).

Under certain environmental conditions, silicified resting cysts, or statospores, are produced by many species. Statospores are formed endogenously, are roughly spherical or ellipsoidal, and have walls that may be smooth or ornamented.

The stomatocyst opening (porus) may be simple, possess a thickened collar, or take the form of a narrow neck. The cyst wall is formed by the deposition of silicate on an internal membrane, and the porus is preformed or produced by resorption of a portion of the cyst wall.

Depending on the species, cytoplasm located outside the cyst wall may or may not be absorbed through the porus, which at maturity is occluded by a pectic plug. During excystment the plug is lost, and one or more amoeboid or free-swimming flagellate cells emerge.

Sexual reproduction is known only in a handful of species. In those cases observed, vegetative cells behave as gametes and fuse apically. The resulting quadri flagellate cell (planozygote) will encyst forming sexually derived binucleate hypnozygotes or stomatocysts.

It is presumed that karyogamy (nuclear fusion) and meiosis occur within the cyst, but these processes have yet to be studied. Depending upon the species, sexual stomatocysts may give rise to one, two, or four vegetative cells.
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7:16 AM
Chytrids
Chytrids
Chytrids are fungi in the phylum Chytridiomycota. They have motile spores and are primarily aquatic organisms.

Like all fungi, chytrids live in their food and have an absorptive mode of nutrition in which they secrete digestive enzymes and absorb the breakdown products.

Chytrids also have cell walls made of chitin, make the amino acid lysine via the amino adipic acid (AAA) pathway, and possess a ribosomal DNA (deoxyribonucleic acid) sequence that places them more closely with other fungi than with any other group of organisms. The feature that sets the mapart from other fungi is the possession of a motile zoospore. All other fungi produce spores without flagella.

Characteristics

Aposteriorly oriented, whiplash-type flagellum is the feature that unites all the organisms in the division Chytridiomycota within the kingdom Fungi. As absorptive heterotrophs, they live either as saprophytes, growing on dead organic matter, or as parasites in living plants, other fungi, insects, or algae.


The vegetative organism may take the form of a spherical structure, with or without branching rhizoids, on the surface of substrate or host or may send mycelial threads through the material in which it is living.

Asexual reproduction occurs by a variety of means described below. Sexual reproduction is known to exist in several types of chytrids and in some species involves the alternation between a gamete-producing phase and a spore-producing phase.

The sporangia that produce the motile zoospores develop in a variety of ways. Two features are used to characterize development: the fate of the nucleus upon encystment of the zoospore and the number of zoosporangia produced from a single zoospore.

The three most common types of thallus development are endogenous-monocentric, exogenous-monocentric, and exogenous-polycentric. Endogenous-monocentric development occurswhen the zoospore nucleus stays within the encysted zoospore wall, undergoes mitosis, and produces a single zoosporangium.

Exogenous-monocentric development occurs when the zoospore nucleus migrates into the germ tube, undergoes mitosis, and produces a single zoosporangium. Exogenous-polycentric development occurs when the zoospore nucleus migrates into the germ tube, undergoes mitosis, and spreads to many locations for zoosporangium production.

The phylum-defining zoospore may be one of four basic morphological types. Though the types are determined by electron microscope, the morphological type can be recognized using light microscopy with experience. The four morphological types are the basis of classification at the ordinal level as described below.

Ecology and Habitats

Because chytrids are absorptive heterotrophs, they grow in their food, digesting complex food molecules and absorbing the simpler breakdown products. When growing in dead material, these fungi are saprophytes and are decomposing organisms in ecosystems. Because the zoospore requires water for dispersal, these fungi are found in aquatic environments.

However, they also can be found in soils that are wet with soil water. Chytrids also can live within living organisms as parasites, causing major declines in populations. The gut chytrids, Neocallimastigales, live in the rumina (stomachal cavities) of herbivorous mammals.

Taxonomy

Taxonomy
Taxonomy
There are approximately eight hundred species of chytrids, arranged in five orders. Taxonomy of the different orders is based on the ultrastructure of the zoospore.

Ultrastructure features used in taxonomy include the presence or absence of a connection between the nucleus and the kinetosome by microtubules; whether ribosomes are dispersed or collected into a mass surrounded by membranes; the degree of organization of the microbody-lipid complex (MLC); the location and number of lipid globules; and presence or absence of a rumposome—a honeycomblike organelle of unknown function. The main characteristics of the five orders are described below.

Chytridiales. During examination of the main features of the zoospore—lipid globule, microbody, mitochondria, and nucleus—the nucleus seems to occupy whatever space is left over within the zoospore.

Rootlet microtubules are located within the plasma membrane connecting the kinetosome to the rumposome. Ribosomes are gathered in the center of the cell, enclosed within membranes. In the MLC, the posteriorly located lipid globules are in close association with the microbody, mitochondrian, and rumposome.

Spizellomycetales. The nucleus of the zoospore is close to the kinetosome or, if separated, is connected to it viamicrotubules or a rhizoplast. Rootlet morphology is variable, and ribosomes are scattered throughout the cytoplasm.

The MLC has a loose association of the microbody and lipid at the anterior end of the zoospore with the mitochondria located toward the rear. There is no rumposome. Ribosomes are dispersed throughout the zoospore.

Neocallimastigales. Neocallimastix and other genera of the order are uniflagellate or multiflagellate and live in the rumen of herbivorous mammals. Because they live in this unique environment, rumen chytrids are obligate anaerobes.

The zoospores lack any of the MLC organelles and the rumposome. All these anaerobic fungi are cellulolytic and digest plant cell walls of the food upon which sheep and cattle feed.

Monoblepharidales. The zoospores have a centrally located nucleus that is not connected to the kinetosome. Microtubules extend randomly into the cytoplasm from the kinetosome.

The MLC has a rumposome in close association with a microbody and anteriorly located lipid globules. The ribosomes are centrally located, surrounding the nucleus. These fungi have amycelial growth form and reproduce sexually by producing amotilemale cell and a nonmotile egg cell.

Blastocladiales. A nuclear cap consisting of ribosomes encased within a membrane located anteriorly to a cone-shaped nucleus and a single largemitochondrian with a side body complex are the two most distinctive features of these fungi. Some of these fungi produce mycelial growth forms, whereas others produce the saclike zoosporangium with rhizoids.

Evolutionary History

Evolutionary history of the chytrids can be traced back to the Pennsylvanian period through fossil evidence. Sequential analysis of the small subunit ribosomal DNA gene from fifty-four chytrids indicates that the Chytridiomycota are related to other fungi and that there are natural groups within the division: Blastocladiales, Monoblepharidales, and Neocallimastigales.

Despite the diversity of the data, the monophyletic nature of the Chytridiales and Spizellomycetales is not rejected. The DNAgroupings closely resemble groupings based on zoospore ultrastructure.

Representative Organisms

Allomyces is a mycelial member of the Blastocladiales, which is interesting because it has an alternation of generations between a gamete-producing thallus (gametothallus) and a spore-producing thallus (sporothallus).

In all organisms with alternation of generations, the gametothallus produces gametes by mitosis in gametangia. The gametes are distinguished by size, the male being smaller than the female.

The motile male gamete is chemotactically attracted to the hormone sirenin, which is produced by the female gametes and enables fertilization. Upon fertilization, the zygote nucleus undergoes mitosis as the germ tube develops into mycelia without cross walls.

The dichotomously branched mycelia of the sporothallus produce two types of sporangia. The thin-walled sporangia produce diploid spores by mitosis. These diploid zoospores are responsible for increasing numbers of Allomyces in its habitat.

The sporothallus also can produce a thick-walled sporangium capable of with standing harsh environmental conditions. Zoospores in this sporangium are produced by meiosis. When these haploid zoospores geminate, the nucleus divides by mitosis and spreads throughout the dichotomously branched mycelia. The life cycle of the fungus now is completed.

Batrachochytrium is interesting because it parasitizes frogs. Within the last decade, declines in populations of frogs around the world have been described. Batrachochytrium dendrobatidis is responsible for this chytridiomycosis in amphibians, including salamanders.

Blastocladiella is a developmental biology tool. The thallus has the exogenous, monocentric developmental pathway resulting in a rhizoidal system with a single thin-walled, colorless sporangium or a single thick-walled, resistant sporangium.

The chemical environment of the developing thallus determines which sporangium is produced. High carbon dioxide levels favor the development of the thick-walled sporangium.

This shift from a thin-walled sporangium pathway to a thick-walled sporangium pathway has been traced to a disruption of the Krebs cycle. This organism is one of a few nongreen organisms in which light promotes the growth of the organism.

Coelomomyces is a mycelial member of the Blastocladiales that parasitizes invertebrate animals. Coelomomyces alternates between a haploid gametothallus and a diploid sporothallus.

The unique feature of Coelomomyces is that each phase is specific for a different host. The diploid sporothallus parasitizes mosquitoes and grows as wall-less mycelia within the hemocoel of the mosquito larvae. Coelomomyces has been studied as a possible mycoinsecticide against mosquitoes.

Difficulty in using Coelomomyces as a mycoinsecticide occurred until the discovery of the fact that an alternate host was required to achieve completion of the life cycle. The zoospores produced by the thick-walled sporangium within the mosquito are produced by the process of meiosis and are haploid.

The haploid zoopore must infect a microcrustacean copopod or ostracod in order for the gametes to be produced. The haploid zoospore develops into the gametothallus, which produces the motile gametes. The resulting zygote will infect mosquito larvae, completing the life cycle.
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7:03 AM
Circadian Rhythms
Circadian Rhythms

Circadian rhythms in plants are phases of growth and activity that appear in regular, approximately twenty-four-hour, cycles.

Biological activities that cycle in approximately twenty-four-hour intervals are called circadian rhythms (from the Latin circa, meaning “about” and dies, meaning “a day”). Circadian rhythms allow plants to anticipate environmental cycles and to coordinate their activities with them.

Circadian rhythms are not simply responses to changing external conditions, as they continue even when a plant is placed under constant conditions. This continuation indicates that circadian rhythms are controlled by endogenous (internal) timing mechanisms, collectively referred to as the biological clock.

Plant circadian rhythms include cycles in gene regulation, enzyme activity, leaf movements, flower opening, and stomatal opening.Circadian rhythms also interact with photoperiodism in the control of major developmental processes, such as dormancy and the induction of flowering.


History

In 1729 the French astronomer Jean-Jacques Dortous de Mairan discovered the endogenous nature of circadian rhythms when he looked at the sleep movements of leaves of the sensitive plant, Mimosa, known as nyctinastic leaf movements. Mimosa leaves fold closed at night and open during the day.

It had been thought that these leaf movements occurred in response to external cycles of light and darkness. De Mairan examined the plants under constant environmental conditions and discovered that the nyctinastic movements of the leaves continued.

This was the first description of a biological activity with an endogenous circadian rhythm. Current models for how plants accomplish circadian rhythms are divided into three parts: entrainment, biological clock, and output pathways.

Entrainment

The synchronization of circadian rhythms to the cycles of the outside world is accomplished via input pathways and is referred to as entrainment. In nature, circadian rhythms are entrained primarily by light or temperature cycles to have periods of twenty-four hours.

It is essential that circadian rhythms be entrained, because without synchronization of the biological clock with environmental cycles, the advantages of circadian rhythms would be lost.

Biological Clock

The biological clock is also referred to as the central oscillator and the pacemaker. It is endogenous and self-sustaining. Although circadian rhythms are entrained by external stimuli, they continue in the absence of external cycles.

Under artificially constant conditions, circadian rhythms do not maintain twenty-four-hour periods but revert to free-running periods that are usually between twenty-one and twenty-seven hours. The molecular mechanisms of the biological clock remain unknown, but they are thought to include autoregulatory feedback mechanisms.

An interesting feature of the biological clock is that the free-running period is generally insensitive to changes in temperature. Most chemical and biological processes are affected by temperature changes; higher temperatures make them go faster, and lower temperatures make them go slower.

Biological clock
Biological clock

That the biological clock is able to compensate for temperature changes and maintain time keeping functions is important to plants experiencing extreme changes in temperature.

Output Pathways

The output pathways, or “hands” of the biological clock, are the measurable rhythms exhibited by the plant. Known circadian rhythms range from the subcellular level to the cell and tissue level to the developmental level.

Subcellular Level

Subcellular circadian rhythms include cycles in gene regulation (at the levels of transcription, transcript abundance, translation, and post-translational modification), calcium signaling, and enzyme activity. One well-characterized rhythm is the rate of carbon dioxide assimilation in plants with CAM (crassulacean acid metabolism) photosynthesis.

Such plants open their stomata at night to allow for gas exchange, fixing carbon dioxide into an organic acid that is stored in the vacuole. During the day, the plants close their stomata (presumably to conserve water) and continue photosynthesis using carbon dioxide released from the organic acids.

The circadian rhythm of carbon dioxide assimilation in CAM plants is controlled by rhythmic changes in the activity of the enzyme (PEP carboxylase) that fixes carbon dioxide into the organic acid.

Cell and Tissue Levels

Cell- and tissue-level circadian rhythms include those controlled by cycles in cell expansion and contraction, such as the obvious rhythms of leaf and petal movements and the opening and closing of stomata.

Leaf movements are brought about by a cycling in the expansion and contraction of specialized cells in a region at the base of the leaf that is called the pulvinus. Nyctinastic leaf movements presumably allow a plant to maximize light interception for photosynthesis.

Many plants open their flowers in the morning and close them at night. Other plants open their flowers in the afternoon (such as the four o’clocks, Mirabilis jalapa), in the evening (evening primrose, Oenothera biennis), or even at night (the bat-pollinated cactus Cereus).

These cycles are important for timing pollen availability with the activity of insect, bird, and mammal pollinators. It is essential that flowers of the same species be open at the same time of day or night to promote outcrossing that results in increased genetic variation.

Circadian cycles of stomatal opening and closing allowa plant to balance carbon dioxide uptake with water loss. Plants with CAM photosynthesis open their stomata at night, in contrast to plants that carry out C3 and C4 photosynthesis, which open their stomata during the day. Other known tissue-level circadian rhythms include hypocotyl elongation, nectar secretion, and hormone synthesis.

Developmental Level

Developmental processes that depend on interactions with circadian rhythms and the biological clock include the photoperiodic control of flowering and dormancy.

These photoperiodic responses rely on the ability of a plant to measure relative amounts of light and darkness within each twenty-four-hour period. It remains unknown whether one biological clock controls both photoperiodism and circadian rhythms.
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11:22 AM
Cladistics
Cladistics
Cladistics is a quantitative method of classification of plants that attempts to recover evolutionary relationships, based on observable characters.

Since the dawn of history, humans have classified plants. In primitive cultures classifications were by economic use, such as food, clothing, medicine, and shelter. Later the form (morphology) of a plant became important, for example, trees, shrubs, or herbs.

Carolus Linneaus considered the similarity of floral parts to be critical, and this formed the basis of his classification system. Each of these systems is said to be “artificial.” That is, the classification was solely for a human purpose and did not attempt to indicate genetic relationships between plants.

Since Charles Darwin, the goal of plant systematics has been to develop a “natural,” phylogenetic classification, one that represents the natural relationships of each species to all others. Cladistics was developed as a method to construct phylogenetic classifications.

A Brief History


Three systems have evolved to aid systematists (scientists who study the phylogenetic relationships of organisms) in their work. Traditional phylogenetics was based on intuition and involved the “art and science” of character weighting.

The scientist studied a group of plants and decided which characters he or she thought were important. Evolutionary relationships were then based on these characters. Individual bias led to disagreements that could not be resolved objectively.

Computer-assisted numerical approaches permitted systematists to employ a more objective methodology and analyze large quantities of data, gathered from a variety of sources that range from traditional morphology to the most sophisticated molecular techniques.

The earliest attempt, phenetics, used computers to determine the degree of total similarity between taxa. Unfortunately, this ignored both parallel and convergent evolution.

The methods of cladistics were first formalized in the 1950’s and 1960’s by Willi Hennig. This approach requires three assumptions to be met: evolution occurs; evolution is monophyletic (that is, lineages derive from a common ancestor); and characteristics passed from generation to generation are either modified or not.

Although phylogenetics is concerned with genealogical relationships, the latter cannot be observed; rather, they must be inferred from observable characters (morphological, biochemical, behavioral, and so on) in much the same way as one infers genotypes when constructing a family pedigree.

Cladistics is a quantitative method that attempts to recover evolutionary relationships, based on observable characters, and presents the resulting phylogeny in the form of a treelike diagram called a cladogram.

When many different organisms are being classified and when many different characters are being analyzed simultaneously, alternative cladograms may result.

The most parsimonious tree (the cladogram requiring the fewest evolutionary changes) is generally preferred, because it is assumed that the simplest pathway is the one most likely to reflect the evolutionary history of the plants being examined.

Constructing a Cladogram

The most important decision to make before beginning construction of a cladogram to represent the relationships among a group of plants is the choice of an appropriate outgroup.

The outgroup cannot belong to the group of plants being analyzed, but it should be closely related. Much of the work of a phylogenetic study is determining an appropriate outgroup to be used for comparisons.

The next step involves construction of a character matrix. A character is any feature of a plant. It may be an observable morphological or biochemical feature or an ecological or physiological attribute.

Every useful character will have more than one character state. For instance, the character “root type” may have the character states “taproot,” “fibrous root,” or “adventitious root.”

Characters having a common origin are called homologous. Cladistic analysis recognizes two types of homologies: plesiomorphies and apomorphies. Plesiomorphies are considered to be the primitive state of a character; that is, the character is unchanged from the ancestral condition.

Plesiomorphies are determined by comparison of the character states in the members of the taxa being investigated with the character state in the outgroup. A character state found in both the outgroup and the taxa being examined is considered to be plesiomorphic.


Any modification of the character state is considered to be apomorphic; thus, apomorphies are derived from plesiomorphies. Apomorphies shared by two or more taxa are called synapomorphies. Identification of synapomorphies, assumed to be derived from increasingly recent common ancestors, provides the basis for constructing cladograms.

Qualitative Approach

The first step toward a qualitative approach to constructing a cladogram is to examine the character matrix and list groupings of taxa according to the apomorphic trait for each character. Next, one character to begin the tree is chosen.

Any character will do, but it is simplest to begin with a character in which only the outgroup has the plesiomorphic state and all ingroup taxa share the same apomorphy. For instance, a conifer might be the outgroup for classifying flowering trees.

The plesiomorphic reproductive structure would be a cone, and the synapomorphy shared by all ingroup members would be flowers. The tree would have the conifer at the base, with a single line extending to the right to a branch point (node) from which all ingroup members diverge.

The character state “flower” would be placed on the line between the conifer and the node, indicating that the shared character state, flowers, evolved prior to the divergence of ingroup taxa from one another.

Next, a second character is added to the existing tree. For instance, the conifer and dicot trees would all share the plesiomorphic character of a taproot, but monocot trees, such as palms, would have fibrous roots.

The tree should now be extended to the right to form a second node with the character state “fibrous roots” added to the new stem segment and the monocot trees branching off the second node.

The monocot taxa diverged from each other after fibrous roots evolved. The dicots do not have fibrous roots, so they are diagramed at the node to the left of “fibrous roots.” The tree is continued by the addition of one character at a time until all have been used.

Quantitative Approach

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The qualitative approach becomes increasingly difficult as the number of taxa and number of characters are increased. The advantages of the quantitative approach are that the process can be automated and human bias can be minimized. The following example illustrates “by hand” the way computers can be programmed to produce a cladogram.

The first step is to code the character matrix to produce a numerical matrix for analysis. Plesiomorphic characters in the data matrix are coded as 0; different apomorphic character states are coded as successive integers, 1, 2, 3, and so on.

The simplest cladogram consists of a Y-shaped diagram representing three taxa, two from the group being studied and a third being the outgroup. The outgroup is placed at the bottom and serves to “root” the tree. The two ingroup species are located at the top of each arm.

The point where the two arms diverge is a node and represents the ancestral taxon derived from the outgroup that gave rise to both ingroup taxa—it represents the common ancestor of the ingroup taxa. A numerical algorithm computes what the character states of this ancestral species must have been.

Additional taxa can now be added to the cladogram, one at a time. A series of new trees are constructed in which the new taxon is added between each existing taxon and each existing node.

There are three places a fourth taxon could be added to the simple tree: between the root and the node, between the node and the first ingroup taxon, and between the node and the second ingroup taxon.

An algorithm computes which of the three possible trees is the most parsimonious, and this tree is used as the basis for adding the fifth taxon (in one of now five possible positions between the four existing taxa and the two nodes). This process is continued until all taxa have been added to the tree and the cladogram is complete.

10:18 AM
Climate and Resources
Climate and Resources
Climate is described by the average of weather conditions at a place or in a region, usually recorded as both the mean and the extremes of temperature, precipitation, and other conditions.

Resources are the factors and characteristics of the natural environment that people find useful, including climate, land, soil, water, minerals, and wild vegetation. Thus, climate itself is a resource, affecting the character of the plant life and other resources it supports.

The nature and distribution of wild vegetation are to a large degree the products of climate: the temperature, moisture, solar radiation, and other environmental conditions that characterize a region. The major global vegetation types that accompany forest, shrub, grassland, desert, rain forest, tundra, and other biomes reflect climatic controls.

Solar radiation is the basic determinant of climate. The sun’s rays are vertical at some time of the year only in the tropics, between the Tropic of Cancer (23.5 degrees north latitude) and the Tropic of Capricorn (23.5 degrees south latitude).


These lines determine where the greatest heat supply is found; regions poleward of about 40 degrees north and south latitudes actually have a net loss of reradiation to outer space and depend upon a heat supply from the tropics, which is carried poleward by the general circulation of the atmosphere. The general circulation is the average of wind flow at the surface of the earth and is driven by the surplus of solar radiation in the tropics.

Equatorial Climates

By definition, tropical climates do not experience freezing temperatures, have the least variation in length of day, and consequently experience the least “seasonality” of any latitudes.

Equatorial Climates
Equatorial Climates
Seasons in the tropics are characterized more by precipitation contrasts—“dry” and “wet”—than by summer and winter temperatures. The greatest combination of heat and moisture resources on the earth’s surface, especially important in creating the conditions under which tropical rain forests flourish, is near the equator.

The depth to which rock and soils are weathered and leached (mineral plant foods dissolved and removed by groundwater flow) is greater near the equator than elsewhere on the earth’s surface. Continuous high temperatures work against carbon storage in the soils.

Under wild vegetation conditions, where the rain forest canopy protects soils from rain drop impact, erosion rates are not as high as one would expect from the intense rain showers. On sloping land, however, the soils become saturated and flow down slope, often catastrophically in landslides.

Where wild vegetation has been removed by human activity, such as farming or development of urban centers, erosion and mass wasting (landslides) are exacerbated during rainy seasons and cause considerable loss of life and property damage.

With increasing distance from the equator, the tropics experience more pronounced seasons, particularly in moisture resources. Precipitation totals decline, and drought risk increases.

Dry seasons are expected annually because of the shifting of the general circulation of the atmosphere. The timing and extent of this shift determine whether a region experiences drought.

East and South Asia are most affected by shifting atmospheric circulation and the resulting wet and dry seasons. Africa also has pronounced wet and dry seasons.

Droughts in this part of the world result in famine: An estimated one million people died in the Sahelian droughts of the late 1960’s and 1970’s. Thus climate must be defined both in terms of averages and of extremes. Extremes result in hazards that have dire consequences for the inhabitants of the affected region.

The probability of drought increases as precipitation averages decrease. Additionally, most tropical rainfall takes the form of intense thunder showers, which are spatially highly variable.

One farm may be drenched by rain while its neighbors continue to be tormented by drought. In addition to drought risk on the margins of the tropics, a major climatic hazard is the tropical cyclone, also called a hurricane or typhoon.

Cyclones rarely affect the equatorial zone but frequent the tropical transition to the subtropics and midlatitudes. Movement of tropical cyclones is easterly in their early and middle stages, following the general circulation known as the trade winds.

The Subtropics

The Subtropics
The Subtropics
The climates that exist in the subtropics, poleward of the tropics, depend on the side of the continent: West sides are deserts or subtropical drylands; east sides are the humid subtropics, a transition zone with cooler temperatures and more risk of frost with greater distance from the equator. The humid subtropics are subject to occasional easterly flow weather systems, including tropical cyclones.

While cyclones represent a serious hazard, claiming both lives and property, these easterly systems also deliver moisture and thus reduce the possibility of drought. The generally warm temperatures and moist conditions make these climates some of the most productive for crop growth, exceeding the potential of the tropics.

In the subtropics, leaching of soils and high erosion rates on cleared fields are nearly as great a problem as in the tropics.

The west coast drylands, which include all the world’s major deserts-Sahara, Atacoma, Kalahari, Australian, and North American—are a consequence of the general circulation of the atmosphere, which in these locations makes the swing from the prevailing westerlies of the middle latitudes to the easterly trade winds.

In the process, high atmospheric pressures prevail, and winds are descending or subsiding, and therefore warming—just the opposite of the conditions required for rainfall.

Drylands may extend deep into the continents, as in North America and especially in Africa and Asia. The dryness of the Sahara blankets the Middle East and extends northward into Central Asia.

Temperatures along the equator ward flank of these five major dryland zones are tropical, and where irrigation water is available, tropical plants may be grown. Most of the drylands are subtropical or midlatitude, and thus they experience frost as well as drought hazard.

Weathering and erosion are appreciably less in the drylands, owing to the absence of moisture. Leaching of the soils is virtually absent. Instead, salts in the soils can build up (salinization) to levels that are toxic to most plants—another climate-related hazard.

The Midlatitudes

The Midlatitudes
The Midlatitudes
The midlatitudes extend from the subtropics to the polar climates of the Arctic and Antarctic. Temperatures follow a transition from warm on the equator ward flank to too cold for agriculture nearer the poles. This is the realm of the westerlies, with extratropical cyclones delivering most of the weather.

It is a zone of contrasting conditions, year by year and day by day, ranging from warmer than average to colder than average, from too humid to too dry on the inland dryland border. The hazards of extreme temperature and precipitation often dominate life, as tropical and polar air masses converge to create the cyclones that march from west to east.

Drought risk is most important on the dryland border and results in the world’s great grasslands. Summer heat may be a hazard on occasion. Nearly every winter brings storms with freezing rain, high winds, and heavy snowfalls, particularly on the eastern sides of the continents.

The eastern sides are also afflicted with intense summer storms, such as the tornadoes of North America (a winter phenomenon in the adjoining humid subtropics) and the tail ends of hurricanes and typhoons, as these storms become caught up in westerly circulation and curve poleward again.

The Arctic fringe of the mid latitudes is too cool for significant agriculture but yields the great subarctic forests of Canada, Scandinavia, and Russia.
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Clines
Clines
A cline is one form of geographic variation in which characteristics of a species change gradually through the species’ geographic range.

Many plant and animal species have populations that differ in terms of their morphological, physiological, and biochemical characteristics. A species is generally defined as a group of organisms that have the potential to interbreed and produce fertile offspring.

A population is defined as a group of organisms which are actively interbreeding. The following example will clarify the relationship between species and populations and simultaneously introduce geographic variation.

Geographic Variation

The ponderosa pine (Pinus ponderosa) occupies a broad geographic range in western North America. Leaves (needles) of ponderosa pines in the Rocky Mountains are bundled into groups of two or three, and cones of these trees are more than 9 centimeters long.


In contrast, leaves of ponderosa pines in southern Arizona and northern Mexico are bundled in groups of five, and their cones are less than 9 centimeters long. These differences constitute geographic variation which has developed because reproduction between Rocky Mountain ponderosa pines and Arizona-Mexican ponderosa pines was restricted because of geographic separation.

Despite their differences, the two groups belong to the same species because they could produce fertile offspring if their geographic separation were overcome. However, they are members of different populations because they are not currently interbreeding. They are different populations of the same species.

Geographic Variation
Geographic Variation
Such geographic variation occurs in many species with broad geographic ranges and is often due to differences in the environmental conditions under which the separate populations exist.

The different environments select for different genetic adaptations, resulting in hereditary variation. If such geographic variation occurs gradually over the range of the species, it is clinal variation.

Clinal Geographic Variation

In the foregoing example, the geographic variation is too abrupt to be considered clinal. However, ponderosa pines in the Sierra Nevada of California do show clinal geographic variation.

The pines at the base of the mountains grow appreciably larger than the pines growing at the highest elevation on the mountains. The change in size is gradual; ponderosa pine trees become progressively smaller as elevation increases.

By taking seeds from trees at several elevations and planting them at the same elevation, scientists showed this size variation to be hereditary. Although all the trees were grown under the same conditions, the largest trees grew from the seeds collected at the base of the mountains, and tree size decreased as the elevation of seed origin increased.

The advantages to being small in the relatively harsh environment of the high mountains and tall at the mountain base were important enough to code tree size into the trees’ genes. The yarrow (Achillea lanulosa) and a number of other plant species show similar clinal variation with elevation in mountains.

In clinal variation, populations are not completely separated from one another, and individuals from adjacent populations do interbreed. However, reproduction between populations is not as common as reproduction between members of the same population. As a result, slight differences between adjacent populations are maintained.

Interestingly, in some clines members of the two extreme populations (the populations at the two ends of the cline) may not be able to interbreed and produce fertile offspring.

They are still considered to be members of the same species because they exchange genes through the intermediate populations. The seaside goldenrod (Solidago sempervirens) illustrates this. It grows along the Atlantic coast of North America and displays a cline in flowering time.

Canadian plants flower in August, plants in the middle Atlantic states flower in September and October, and those in Florida do so in November. These are genetically controlled flowering times, so even if grown together, the plants from Florida and Canada could not interbreed.

However, because Canadian plant flowering times overlap those in the northern United States (which overlap those in the central United States, which overlap those to their south, which overlap those in Florida), there is interbreeding between all adjacent populations and, indirectly, between the Canadian plants and the Florida plants.

If the cline were to be subdivided into two or more species, where would the separations be drawn without separating interbreeding organisms into different species? The simplest solution is to consider all members of the cline to be members of the same species.

Local Clinal Variation

Local Clinal Variation
Local Clinal Variation
Great distances are not always required to establish clines. White clover (Trifolium repens), a European native which has been introduced all over the world, affords an example. Some white clover plants release cyanide when parts of the plant are eaten by grazers, such as snails and slugs.

Others do not. The cyanide protects the plant from further grazing because it is toxic to the grazers. However, the cyanide-releasing form of clover suffers more frost damage than clover plants that do not release cyanide. Plants protect themselves from the cyanide by sequestering it into cellular compartments.

Frost damage occurs when cyanide is released into the plant cells after those compartments are ruptured by ice crystals. Cyanide-storing plants also grow more slowly than forms that do not store cyanide, because some energy that could otherwise be used for growth is required to sequester the cyanide.

Latitudinal and elevational temperature gradients generate clines in the production of cyanide, with greater cyanide production at lower elevations and latitudes. More frequent freezing results in more frequent cyanide damage, and low temperatures result in less grazing, because grazers are not as active.

Plants that do not go to the expense of storing cyanide are favored under those conditions. This is a classic geographic cline. However, changes in grazing pressure overmuch smaller distances also generate clines in cyanide storage.

Grazing pressure changes over meters when white clover grows in a garden protected by pesticides and in an adjacent, unprotected field. The result is a cline in cyanide storage by white clover very similar to the geographic clines discussed above but on a scale of meters.
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Plant cloning is the production of a cell, cell component, or plant that is genetically identical to the unit or individual from which it was derived.

The term“clone” is derived from the Greek word klon, meaning a slip or twig. Hence, it is an appropriate choice. Plants have been “cloned” from stem cuttings or whole-plant divisions for many centuries, perhaps dating back as far as the beginnings of agriculture.

Historical Background

In 1838 German scientists Matthias Schleiden and Theodor Schwann presented their cell theory, which states, in part, that all life is composed of cells and that all cells arise from preexisting cells.

This theory formed the basis for the concept of totipotency, which states that since cells must contain all of the genetic information necessary to create an entire, multicellular organism, all of the cells of a multicellular organism retain the potential to recreate, or regenerate, the entire organism. Thus was the basis for plant cell culture research.


The first attempt at culturing isolated plant tissues was by Austrian botanist Gottlieb Haberlandt at the beginning of the twentieth century, but it was unsuccessful. In 1939 Professor R. J. Gautheret and colleagues demonstrated the first successful culture of isolated plant tissues as a continuously dividing callus tissue.

The term callus is defined as an unorganized mass of dividing cells, such as in a wound response. It was not until 1954, however, that the first whole plant was regenerated, or cloned, from a single adult plant cell by W.H.Muir et al.

Thereafter, an increased understanding of plant physiology, especially the role of plant hormones in plant growth and development, contributed to rapid advances in plant cell and tissue culture technologies in the 1970’s and 1980’s. Many plant species have been successfully cloned from single cells, thus demonstrating and affirming the concept of totipotency.

Horticulture

By far, the greatest impact of cloning plants in vitro (Latin for “in glass,” meaning in the laboratory or outside the plant) has been on the horticultural industry. In the 1980’s plant tissue culture technologies propagated and produced many millions of plants.

Today, many economically important plants are commonly propagated via tissue culture techniques, including vegetable crops (such as the potato), fruit crops (strawberries and dates), floriculture species (orchids, lilies, roses, Boston ferns), and even woody species (pines and grapes).

The advantages of plant cell, tissue, and organ culture technologies include a more rapid production of plants, taking weeks instead of months or years. Much less space is required (square feet instead of field plots).

Plants can be produced year-round, and economic, political, and environmental considerations that hamper the propagation of regional or endangered plant species can be reduced. The disadvantages include the high start-up costs for facilities, the skilled labor required, and the need to maintain sterile conditions.

Two other significant considerations must be considered as a result of plant propagation technologies. As illustrated by the Irish Potato Famine of the 1840’s, the cultivation of whole fields of genetically identical plants (monoculture) leaves the entire crop vulnerable to pest and disease infestations.

The second important consideration when generating entire populations of clones, especially using tissue culture technologies, is the potential for introducing genetic abnormalities, which then are present in the entire population of plants produced, a process termed somaclonal variation.

Biotechnology

An absolute requirement for genetic engineering of plants is the ability to regenerate an entire plant from a single, genetically transformed cell, thus emphasizing the second major impact of plant cell culture technologies.

In 1994 the U.S. Food and Drug Administration (FDA) approved the first genetically modified whole food crop, Calgene’s Flavr Savr tomato. This plant was produced using what is termed anti-sense technology. One of the tomato’s genes involved in fruit ripening was reversed, thus inactivating it and allowing tomatoes produced from it to have significantly delayed ripening.

Although no longer commercially marketed, the Flavr Savr demonstrated the impact of genetic engineering in moving modern agriculture from the Green Revolution into what has been termed the Gene Revolution.

Other examples of agricultural engineering exist today, such as Roundup Ready Soybeans, engineered to resist the herbicide used on weeds where soybeans are grown, and BT Corn,which contains a bacterial gene conveying increased pest resistance.

Since 1987, the U.S. Department of Agriculture (USDA) has required field testing of genetically modified crops to demonstrate that their use will not be disruptive to the natural ecosystem.

To date, thousands of field trials have been completed or are in progress for genetically modified versions of several crop species, including potatoes, cotton, alfalfa, canola, and cucumbers.
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