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Chapter 12: Plant Behavior and Hormones Regulating Growth: Plant Hormones Plant cells are in constant chemical communication with one another and with their environment. They recognize and respond to stimuli of many kinds, using a system of chemical messengers that receive and transmit the stimuli via ordinary body cells (unlike the highly specialized cells of animal nervous systems). Control of the plant system apparently resides in the genes of each cell, which are turned on and off by the chemical messages they receive. The response may be stimulatory (initiating cellular division and enlargement, for example) or inhibitory (such as stopping a metabolic process). The chemical messengers are hormones , organic substances manufactured in small amounts in one tissue and usually transported to another where they initiate a response. (A few act in the tissues where they are produced.) The hormone molecule itself carries little information and produces a reaction only when it binds to appropriate receptor molecules at the response site. Plants, in comparison to animals, have both fewer hormones and fewer kinds of responses. Plant hormones, however, usually act in combination, thus producing more varied responses than if acting individually. The same hormone also can produce different effects when acting in different tissues or in different concentrations in the same tissue. The developmental stage of the plant additionally determines what effects the hormone activates. Growth and development depend upon a successful coordination of the activities of hormones, not just the presence or absence of individual ones. Types of Plant Hormones There are five general classes of hormones: auxins, cytokinins, gibberellins, ethylene, and abscisic acid. Auxins An auxin, indole-3-acetic acid (IAA) , was the first plant hormone identified. It is manufactured primarily in the shoot tips (in leaf primordia and young leaves), in embryos, and in parts of developing flowers and seeds. Its transport from cell to cell through the parenchyma surrounding the vascular tissues requires the expenditure of ATP energy. IAA moves in one direction only—that is, the movement is polar and, in this case, downward. Such downward movement in shoots is said to be basipetal movement, and in roots it is acropetal. Auxins alone or in combination with other hormones are responsible for many aspects of plant growth. IAA in particular: Activates the differentiation of vascular tissue in the shoot apex and in calluses; initiates division of the vascular cambium in the spring; promotes growth of vascular tissue in healing of wounds. Activates cellular elongation by increasing the plasticity of the cell wall. Maintains apical dominance indirectly by stimulating the production of ethylene, which directly inhibits lateral bud growth. Activates a gene required for making a protein necessary for growth and other genes for the synthesis of wall materials made and secreted by dictyosomes. Promotes initiation and growth of adventitious roots in cuttings. Promotes the growth of many fruits (from auxin produced by the developing seeds). Suppresses the abscission (separation from the plant) of fruits and leaves (lowered production of auxin in the leaf is correlated with formation of the abscission layer). Inhibits most flowering (but promotes flowering of pineapples). Activates tropic responses. Controls aging and senescence, dormancy of seeds. Synthetic auxins are extensively used as herbicides, the most widely known being 2,4-D and the notorious 2,4,5-T , which were used in a 1:1 combination as Agent Orange during the Vietnam War and sprayed over the Vietnam forests as a defoliant. Cytokinins Named because of their discovered role in cell division (cytokinesis), the cytokinins have a molecular structure similar to adenine. Naturally occurring zeatin , isolated first from corn ( Zea mays) , is the most active of the cytokinins. Cytokinins are found in sites of
active cell division in plants—for example, in root tips, seeds, fruits, and leaves. They are transported in the xylem and work in the presence of auxin to promote cell division. Differing cytokinin:auxin ratios change the nature of organogenesis. If kinetin is high and auxin low, shoots are formed; if kinetin is low and auxin high, roots are formed. Lateral bud development, which is retarded by auxin, is promoted by cytokinins. Cytokinins also delay the senescence of leaves and promote the expansion of cotyledons. Gibberellins The gibberellins are widespread throughout the plant kingdom, and more than 75 have been isolated, to date. Rather than giving each a specific name, the compounds are numbered—for example, GA1, GA2 , and so on. Gibberellic acid three (GA3 ) is the most widespread and most thoroughly studied. The gibberellins are especially abundant in seeds and young shoots where they control stem elongation by stimulating both cell division and elongation (auxin stimulates only cell elongation). The gibberellins are carried by the xylem and phloem. Numerous effects have been cataloged that involve about 15 or fewer of the gibberellic acids. The greater number with no known effects apparently are precursors to the active ones. Experimentation with GA3 sprayed on genetically dwarf plants stimulates elongation of the dwarf plants to normal heights. Normal- height plants sprayed with GA3 become giants. Ethylene Ethylene is a simple gaseous hydrocarbon produced from an amino acid and appears in most plant tissues in large amounts when they are stressed. It diffuses from its site of origin into the air and affects surrounding plants as well. Large amounts ordinarily are produced by roots, senescing flowers, ripening fruits, and the apical meristem of shoots. Auxin increases ethylene production, as does ethylene itself—small amounts of ethylene initiate copious production of still more. Ethylene stimulates the ripening of fruit and initiates abscission of fruits and leaves. In monoecious plants (those with separate male and female flowers borne on the same plant), gibberellins and ethylene concentrations determine the sex of the flowers: Flower buds exposed to high concentrations of ethylene produce carpellate flowers, while gibberellins induce staminate ones. Abscisic acid Abscisic acid (ABA), despite its name, does not initiate abscission, although in the 1960s when it was named botanists thought that it did. It is synthesized in plastids from carotenoids and diffuses in all directions through vascular tissues and parenchyma. Its principal effect is inhibition of cell growth. ABA increases in developing seeds and promotes dormancy. If leaves experience water stress, ABA amounts increase immediately, causing the stomata to close. Responsive Growth Movements: Tropisms Responsive growth movements toward or away from an external stimulus are called tropisms. If the plant movement is toward the stimulus, it is a positive tropism; away from the stimulus, a negative tropism. Phototropism The tropic response to unidirectional light is called phototropism. In general, shoots grow toward light and hence are positively phototropic; roots grow away from light and are negatively phototropic. Well-known and often-repeated experiments with oat seedlings have shown that the auxin IAA, which causes elongation of cells, migrates to the shaded side of oat coleoptiles. The subsequent differential growth on the two sides causes the coleoptiles to bend toward the light. Although green stems also bend and grow toward the light, in this case an IAA inhibitor prevents cells from elongating on the lighted side, while those on the shaded side continue to elongate; the stem bends toward the light as a consequence of the differential growth. Different wavelengths of light cause differing growth responses. The blue end of the spectrum—wavelengths less than 500μm—is most effective in producing a growth m—is most effective in producing a growth response. Gravitropism Gravitropism is the plant response to gravity. The mechanism of how gravity is sensed by plants is as yet unexplained. None of the numerous hypotheses is fully adequate. Over the eons, plants probably developed several methods to cope with this environmental factor. Shoots are negatively gravitropic, because they grow upward; roots are positively gravitropic—they grow downwards. IAA, calcium ions (Ca2+), and possibly ABA are involved in instigating growth and curvature in many plants. Still to be proven is the long-
Phytochrome Plants make such adjustments by utilizing the pigment phytochrome, which exists in two forms: P r, which absorbs red light, and P fr, which absorbs far-red light. Each can convert to the other when they absorb light. During the day, the two forms convert back and forth (Pr becomes Pfr, and vice versa), until they reach an equilibrium of 60:40 Pfr: Pr in plant tissues. During the night, Pfr slowly converts to Pr or else disintegrates. Pr is stable in the dark. Pfr is the biologically active form, acting as the switch that turns on such plant responses as flowering or seed germination. When the threshold concentration of Pfr is attained, the response is stimulated. Thus, it is the length of the night period, not the day period, that determines the response. Short nights (meaning long days) favor activities that require large amounts of Pfr; conversely, if the night is long (and the day short), more Pfr is converted back to Pr and responses triggered by small amounts of Pfr are favored. Pr, synthesized from amino acids, is the inactive form. Photoperiodic responses Photoperiodism was first studied in relation to flowering. Plants can be described in relation to their photoperiod responses as short- day, long-day, day-neutral , and intermediate-day plants. Plants that flower in late summer and fall are short-day; they have a critical period of light exposure of less than about 16 hours. Long-day plants are summer flowering and have a critical period of longer than 9 to 16 hours. Day-neutral plants flower in photoperiods of any length, while intermediate-day plants flower only in periods neither too long nor too short for the particular plant (that amount of time is different for each plant studied to date but not classifiable as either long-day or short-day). Other photoperiodic responses involving the phytochrome system include seed germination and the early growth of seedlings. Florigen Because hormones control so many metabolic activities in plants, flowering has long seemed likely to be under the control of one or more hormones. Early experiments sought to determine which part of a plant is sensitive to the light that initiates flowering. The results suggested the presence of a substance that moved from the leaves to the flower buds. Although the substance was not identified then—nor has it been isolated now—it was named florigen. Florigen is the hypothetical flowering hormone; it may or may not actually exist. Note that flowering most likely is not controlled by a single hormone, but is the result of a combination of internal and external signals and responses. Dormancy Shoot dormancy Rarely do all factors of the environment remain suitable indefinitely for plant growth. In the temperate latitudes, for example, breaks in the growing season occur when seasons change, bringing reduced temperatures and shorter days in the autumn and winter. In the subtropics and tropics, where temperatures and day lengths remain equitable all year, water availability may fluctuate between a wet and a dry season. Plants have developed mechanisms to survive during such adverse periods. One effective mechanism, used by annual plants, is to produce a photosynthetic and flowering structure rapidly and then sink the resources derived from photosynthesis into seed production and distribution. The plant body is no longer useful and is abandoned after protected embryos are produced. The seeds withstand the changes of the next unfavorable growth period and germinate when environmental stimuli indicate favorable growth conditions. Perennial flowering plants also use the seed mechanism, but some retain their photosynthetic and root structures, merely dropping the most vulnerable parts (leaves) during the unfavorable growth period. When one or more of the plant organs undergoes a period in which the growth processes are slowed down or suspended, that state is termed dormancy. The growth is reactivated when environmental stimuli are received that, in effect, inform the plant that conditions are again suitable for growth. The signals to break dormancy are extraordinarily precise. External stimuli combine with internal signals to ensure that renewal of growth will occur at the most favorable time. Many plants have internal growth inhibitors that decay
slowly over time, such as ABA. Until the inhibitor has dropped to a certain low level, no growth will take place despite external stimuli; both external and internal signals must be correct. Seed dormancy Almost all seeds undergo some period of dormancy—if they did not, they would start to grow in the fruits on the mother plant and defeat their principal purposes: dispersal and survival of the germplasm. The period between the formation of the seed and the time when it will germinate is called the after-ripening period , which may be a few days or months depending on the plant. Seeds of plants native to regions with cold winters almost all require an after-ripening period of cold temperatures before they will germinate. This requirement can be met in horticultural and crop varieties by refrigerating the moist seed for a period of time. This procedure is called stratification. Dormancy of seeds with hard seed coats often can be broken artificially by scarifying the seed— mechanically thinning the seed coat with a file or nicking it with a knife, allowing water and oxygen to penetrate to the embryo. Bud dormancy Woody and herbaceous perennials produce dormant overwintering buds in habitats with cold winters. The buds are miniature shoots with apical meristems, leaf primordia, and axillary buds, the whole enclosed by several modified leaves called bud scales. The scales protect the embryonic tissues of the bud from mechanical injury and insulate them. In many climates the scales prevent the formation of ice crystals in the young tissues. Bud scales also restrict gas exchange and prevent desiccation. They often accumulate growth inhibitors as well. Buds start their growth early in the growing season and by midsummer are completely formed. They then undergo a series of physical and physiological changes in preparation for winter. The process is called acclimation and is triggered primarily by the shorter days of late summer. Plants that have acclimated to winter are said to be cold-hardy. Dormancy is broken in the spring in tree buds by the lengthening days. The buds are the photoperiod receptors. Senescence Senescence is the orderly, age-induced breakdown of cells and their components, leading to the decline and ultimate death of a plant or plant part. The timing of senescence is species-specific and varies among the organs of individual plants. Some species of plants produce short-lived flowers whose petals last for only a few hours before shriveling and dropping off, while the leaves of deciduous plants last through long growing seasons before senescing. Senescence is a metabolic process; therefore, it requires energy. It is not simply the ending of growth. Leaves, for example, move the products of photosynthesis—and their own structural substances—out of leaf tissue into stem and root tissue during senescence and before their vascular connections are severed at abscission. One of the first materials to degrade is the energy-converting pigment chlorophyll. As the bright green color of chlorophyll fades, the yellow-orange colors of the carotenoids become prominent and combine with the red-blue anthocyanins to produce the vivid colors of autumn in the trees and shrubs of the northern deciduous forest. The role of hormones in senescence is not clear. Not only the kinds, but the proportions of each are important. Ethylene promotes abscission of leaves, flowers, and fruits, while IAA retards senescence and abscission. When days shorten in autumn, IAA production decreases, and ethylene production increases, hastening changes in the cells of the abscission zone. When the degradation of the cell wall materials is complete, nothing remains to hold the leaf to the stem, and with any slight disturbance the leaf falls. Some evidence indicates that a senescence factor , presumably an unknown hormone, exists in some plants (like soybeans), but it has yet to be isolated or synthesized.
Figure 1 Figure 2 Meiosis and mitosis have many similarities. There are, however, several fundamental differences. Compare Figure 1 (mitosis) with Figure 2 (meiosis). In meiosis: In Prophase I, homologous chromosomes come together in synapsis and form pairs called bivalents or tetrads (because there are four chromatids in the pair); each bivalent has two chromosomes and four tetrads. In Metaphase I, bivalents align randomly on the equatorial plane, which means that each daughter cell has an equal chance of getting either the chromosome from the sperm or one from the egg. In Anaphase I, the chromosomes separate, each with two chromatids, and move to opposite poles; each of the two daughter cells is now haploid ( n ). There is no S phase, and the chromosomes line up immediately in Metaphase II, their chromatids separate in Anaphase II and in Telophase II new cell walls form around the four haploid cells. (Events of the second division are similar to those of mitosis.) Synapsis in Prophase I is a decisive interval in determining the inheritance of the daughter cells. At this time, genetic recombination can occur; that is, daughter cells may receive combined traits of their two parents rather than simply the trait from one or the other. This is possible because the phenomenon called crossing over often occurs when the chromatids lie together—segments containing similar alleles break apart and rejoin to the corresponding segment of the opposite chromatid, thus mixing the traits from individual parents.
Chapter 14 & 15: Inheritance, Genetics, Genetic Engineering Mendelian Genetics The breeding experiments of the monk Gregor Mendel in the mid-1800s laid the groundwork for the science of genetics. He published only two papers in his lifetime and died unheralded in 1884. The significance of his paper published in 1866 on inheritance in peas (which he grew in the monastery garden) apparently went unnoticed for the next 34 years until three separate botanists, who also were theorizing about heredity in plants, independently cited the work in 1900. During the next 30 years, the universality of his findings was confirmed, and breeding programs for better livestock and crop plants—and the science of genetics—were well under way. At the time of Mendel's work, scientists widely believed that offspring blended the characteristics of their parents, but Mendel's painstaking experimentation suggested this was not so. Remember, no one had yet heard of genes, chromosomes, or meiosis, but Mendel concluded from his breeding experiments that particles or “factors” that passed from the parents to the offspring through the gametes were directly responsible for the physical traits he saw first lost in the offspring's generation, then repeated in the next. Closer still to the actual truth, Mendel even hypothesized that two factors, probably one from each parent, interacted to produce the results. His “factors” were, of course, the genes, which do, indeed, come in pairs or alleles for each trait. Some say Mendel was lucky, others that his reported results are too good to be true, that he (or someone else) must have fudged the data to make them “come out right.” His choice of garden peas was fortuitous. Peas are self-pollinated, and the seven traits he chose to measure are inherited as single factors, so Mendel could establish true-breeding lines for each trait. Thus, he was able to select the parent traits, pollinate the flowers, and count the results in the offspring with no complicating elements. He was mathematically trained, kept accurate records, and applied mathematical analyses (and was among the first to do so with biological materials). Mendel's first law: Law of Segregation Mendel did not formulate his conclusions as laws or principles of genetics, but later researchers have done so. Restating and using modern, standardized terminology, this is the information that developed and expanded from his early experiments. Inherited traits are encoded in the DNA in segments called genes , which are located at particular sites ( loci , singular locus ) in the chromosomes. (Genes are Mendel's “factors.”) Genes occur in pairs called alleles , which occupy the same physical positions on homologous chromosomes; both homologous chromosomes and alleles segregate during meiosis, which results in haploid gametes. The chromosomes and their alleles for each trait segregate independently, so all possible combinations are present in the gametes. The expression of the trait that results in the physical appearance of an organism is called the phenotype in contrast to the genotype , which is the actual genetic constitution. The alleles do not necessarily express themselves equally; one trait can mask the expression of the other. The masking factor is the dominant trait, the masked the recessive. If both alleles for a trait are the same in an individual, the individual is homozygous for the trait, and can be either homozygous dominant or homozygous recessive. If the alleles are different—that is, one is dominant, the other recessive—the individual is heterozygous for the trait. (Animal and plant breeders often use the term “true-breeding” for homozygous individuals.) Geneticists use a standard shorthand to express traits using letters of the alphabet, upper case for dominant, lower case for recessive. Red color, for example, might be R or r so a homozygous dominant individual would be RR , a homozygous recessive individual, rr and a heterozygous individual Rr. Crosses between parents that differ in a single gene pair (such as those that Mendel made) are called monohybrid crosses (usually TT and tt). Crosses that involve two traits are called dihybrid crosses. Symbols are used to depict the crosses and their offspring. The letter P is used for the parental generation and the letter F for the filial or offspring generation. F 1 is the first filial generation, F 2 the second, and so forth. What kinds of crosses did Mendel make to conclude that factors/genes segregate? First of all, he made certain that the plants that he planned to use in the experiment were pure line for the trait—that is, that they bred true for the trait for two or more years. (Peas are self-pollinated so he simply grew the plants and examined their offspring.) Other experimenters omitted this step, which confounded their results. Mendel then made a series of monohybrid crosses for each of the seven traits he had identified using parents of opposite
what would the ratio have been? Right, all tall; that's why breeders today make test crosses back to the homozygous recessive parent to see if their phenotypically dominant individuals are homozygous or heterozygous. Mendel's second law: Law of Independent Assortment Mendel also worked with crosses involving two traits—this is where his luck really entered in. The traits he picked are on separate chromosomes (though, of course, he didn't know this). Had they been on the same chromosomes, the ratios he obtained would not have been possible because the traits would always go together in the same gamete unless some cellular tinkering took place. The mechanisms for figuring out the possible gametes with two traits, filling out the Punnett square, and counting the possibilities are the same—only with more variations possible (see Table 1 for potential numbers). TABLE 1 Possible Two-Trait Genetic Variations Monohybrid Dihybrid Trihybrid n - hybrid No. of different kinds of gametes 2 4 8 2 n Proportion of homozygous recessive F 2 1/4 1/16 1/64 (1/2n)^2 No. of different phenotypes F 2 2 4 8 2 n No. of different genotypes in F 2 3 9 27 3 n Here's what the cross looks like for two of Mendel's traits combined, flower color and pod characteristics. One allele for each goes in each gamete; purple color (P) is dominant over white (p) flowers, and inflated pods (I) are dominant over constricted (i). Self pollinate the F 1 purple flowered, inflated pod plants and what is the F 2 ratio? Not 3:1 anymore. Fill out a Punnett square and see the possibilities. Each gamete gets one allele of each trait, so a dominant purple (P) can have either a dominant inflated pod (I) or a recessive constricted pod (i); ditto the white (p). Thus, four kinds of gametes are possible: PI, Pi, pI, pi and 4 × 4 combinations are possible from the two parents:
The phenotypic dihybrid ratio is 9:3:3:1–9 purple inflated, 3 purple constricted, 3 white inflated, and 1 white constricted. (Geneticists now test their results statistically to see if they approach the theoretical 9:3:3:1 and usually use the χ^2 [chi-square] test.) chi-square] test.) Mendel drew a conclusion on the basis of his dihybrid crosses that is now known as Mendel's second law: the Law of Independent Assortment. It states that during gamete formation the segregation of the alleles of one allelic pair is independent of the segregation of the alleles of other genes. Mendel confirmed this hypothesis further (as he did in the monohybrid crosses) by backcrossing the F 1 dihybrid to the recessive parent. The Punnett square for the backcross looks like this: The phenotypic ratio for the testcross is: 1:1:1:1; that is, 1 purple inflated:1 purple constricted:1 white inflated:1 white constricted— which indicates that the traits have separated and recombined independently of one another. Intricacies of Inheritance Continued breeding experiments, better microscopes, and more scientists working in the field have advanced the knowledge of inheritance in organisms and, at the same time, complicated the simple patterns discovered by Mendel. This article covers some of the intricacies. Linkage and crossing over Shortly after the genetic community accepted Mendel's Law of Independent Assortment, several exceptions to its operation were found. Most of these exceptions were the result of linkage of the genes being studied on one chromosome. When the usual crosses were made (P 1 : parents pure-line dominant for two traits × pure-line recessive for two traits), the F 1 individuals of the cross were all dominant and presumably heterozygous. Selfing (transferring pollen from the anthers to the stigma of the same flower) of the F 1 resulted in no predictable ratios, and never the expected 9:3:3:1. Two phenotypes, those of the original P 1 parents, were in high frequency in the F 2 and two other phenotypes, in low frequency, combined the phenotypes of the two original parents. In searching for explanations for the phenomena, the scientists followed the principle of parsimony —that is, they looked first for the simplest explanation that fits all the facts. In this instance, the simplest interpretation—and the correct one—is that the genes for the traits lie close together on the same chromosome. Linkage might properly explain the high frequencies of two phenotypes, but what of the low frequency, other combinations? The most logical explanation is that during Prophase I of meiosis when the four chromatids of two homologous chromosomes lie close together, crossing over occurs; that is, there is a physical exchange of material between non-sister chromatids and a genetic recombination.
Chapter 16: Evolution Darwin's Theory of Evolution Evolution , as understood by biologists, is the change through time that occurs in populations of organisms in response to changing environments. The changes, coded in the molecules of DNA , are transmitted from generation to generation and over the history of the Earth have resulted in progressively more complex life forms. The name of Charles Darwin and his theory of natural selection are inexorably attached to evolution and, together with the mechanisms of genetics, form the basis of the modern theory of evolution. Simplifying and paraphrasing from Darwin's book, On the Origin of Species by Means of Natural Selection , and adding current interpretations, the main points of his theory are: all life came from one or a few kinds of simple organisms; new species arise gradually from preexisting species; the result of competition among species is extinction of the less fit; gaps in the fossil record account for the lack of transitional forms. These assertions set the stage for the next part of the theory, why life evolves: the number of individuals increases at a geometric rate; populations of organisms tend to remain the same size because the resources are limited, and only the fittest survive; the survivors are variable, and those that survive reproduce, perpetuating the favorable traits. Natural selection, according to Darwin, is similar to artificial selection. The environment acted as the selecting force in natural selection. Unlike the relatively rapid selection pressures instituted by breeders, however, natural selection took long periods of time to accomplish change. Darwin was familiar with the then new conclusions of geologists that the Earth was far older than previously thought, which gave his theory of natural selection sufficient time in which to work. A major problem was an explanation for how the favorable selections were perpetuated. In the 1860s the idea that offspring were blends or mixtures of the traits of their parents, the so-called “blending theory of inheritance,” was unable to accommodate transmittal of favorable adaptations from one generation to the next. With botanist Gregor Mendel's ideas and the development of genetics, the inheritance portion of Darwin's theory no longer posed a problem. Modern Theory of Evolution The neo-Darwin view of evolution incorporates modern understanding of population genetics, developmental biology, and paleontology, to which is being added knowledge of the molecular sequencing of DNA and the insights it provides concerning the phylogeny of life. The major premises of the genetic (synthetic) theory of evolution are: evolution is the change of gene (allele) frequencies in the gene pool of a population over many generations; species (and their gene pools) are isolated from one another, and the gene pool of each species is held together by gene flow; an individual has only a portion of the pool, which came from two different parents, and the portions are different in each individual; the alleles the individual receives are subject to chromosomal or gene mutations and recombinations; natural selection will favor some individuals, who will then contribute a larger portion of their gene combinations to the gene pool of the next generation; changes of allele frequencies come about primarily by natural selection, but migration, gene flow, and chromosomal variations are contributing factors; isolation and restriction of gene flow between subpopulations and their parent populations are necessary for the genetic and phenotypic divergence of the subpopulations.
Chapter 17: Plant Diversity Modern Taxonomy Includes Phylogenetics Systematics is the name for the branch of biology concerned with the study of the kinds of organisms, their relationships to one another, and their evolutionary history. Taxonomy , a term often used interchangeably with systematics, is the part of systematics involved in the description, naming, and classification of organisms. Phylogenetics , another part of systematics, is the study of the phylogeny or evolutionary history of an organism or a group of organisms. Two underlying goals of plant systematics, thus, are to: Find, describe, give unique names to, and organize into categories the species of plants of the world (a goal of taxonomy). Organize plants and plant groups to reflect their evolutionary relatedness and their descent from a common ancestor (a goal of phylogenetics). Systematics today is a vigorous and exciting field that has been given great impetus by the discoveries of molecular biologists, who now are describing organisms at their most fundamental level—the DNA sequences of the cells—and providing the systematists new data on which to base their phylogenetic trees. Phylogenetic trees are the graphic representation of the evolutionary divergences of organisms that put together on the same branches the organisms most closely related, with oldest ancestors near the base, youngest descendants near the top. The trees obtained from the DNA sequences basically trace the history of how the genes have changed through time. Naming Plants Biologists around the world use today a single method with standardized rules to name plants and animals: the bionomial system of nomenclature. The bionomial system of nomenclature The binomial system in use today gives a single name recognizable throughout the world to each individual kind of organism. The scientific name consists of two parts (in Latin): the name of the genus (plural: genera ), plus the name of the particular species. The system originated with Carl Linnaeus in the middle of the eighteenth century as a shortcut to the cumbersome polynomial system then in use that required 12-word descriptions to be written as part of the name. In the binomial system, the scientific name is italicized in print and the genus is capitalized, but the species is not. Lay people often ridicule scientific names as unpronounceable atrocities, but these same scoffers use many genera names with little complaint. Geranium, chrysanthemum, aster, asparagus, primula, begonia, and rhododendron (as well as hundreds of others) are not only common plant names, but genera names as well. Other common names are recognizable as anglicized versions of such genera names as: Pinus, Juniperus, Cyperus, Rosa, Hyacinthus, Tulipa, Lilium and others.
Taxonomic hierarchy The Linnaean hierarchical system (see Table 1 ) is a means to group similar organisms together in levels of increasing inclusiveness from the species at the bottom to the most inclusive—kingdom—at the top. Genera are groups of species, families are groups of genera, and so on up the hierarchy. Taxon (plural: taxa ) is a general name given to the members of any level in the hierarchy; in Table 1. Aster is a taxon or Anthophyta is a taxon or spectabilis is a taxon. TABLE 1 Linnaean Hierarchical System Kingdom Plantae Phylum Anthophyta Class Dicotyledonae Order Asterales Family Asteraceae Genus Aster Species spectabilis common name showy aster scientific name Aster spectabilis Types of Classifications Classifications are orderly ways to present information and, depending upon their objectives, can be artificial, natural, or phylogenetic (phyletic), which includes phenetic and cladistic. Artificial and natural classifications Classifications that use single or at most only a few characteristics to group plants usually are artificial classifications—that is, all the plants in a single group share the same characteristics, but they are not closely related to one another genetically. Popular floras (books to identify plants of a certain area) sometimes group plants using color of their flowers, or their growth form (trees, shrubs, herbs, and so on). Although such books are useful in finding the names of taxa, they provide few clues about relationships among the taxa and hence are not predictive, which means that you can deduce nothing more about the plant other than that it exhibits the characteristics
used to classify it. Natural classifications group together plants with many of the same characteristics and are highly predictive. That is, by enumerating the characteristics of a plant, one can predict the natural group to which it belongs. Taxonomic floras, for example, identify species, genera, and families by listing as many characteristics as possible concerning anatomy, morphology, cytology, ecology, biochemistry, genetics, and distribution. Phylogenetic (phyletic) classifications Phyletic classifications are natural classifications that try to identify the evolutionary history of natural groups. When botanists accepted Darwin's theory of evolution near the end of the last century, the reasons why some groups of plants looked alike became clear: They were related to one another by a common ancestry. The mission of taxonomy since Darwin has become a quest for evolutionary relationships, not just at the lower levels of the hierarchy, but at the upper levels as well. The evolutionary history of a taxon is called its phylogeny. To establish phylogenies, decisions must be made concerning which characteristics are “primitive” and which “advanced”—that is, which taxon is the ancestor of the others. Early phylogenetic classifications were based primarily upon plant morphology and anatomy with great emphasis upon reproductive morphology, which is more stable and less influenced by the environment than is vegetative morphology. Today, taxonomists additionally use the techniques of biochemistry and molecular biology to add details of internal organization and mechanisms to the classifications. But phylogenies, no matter how carefully constructed, are dependent upon someone's interpretation of data, and herein lies the problem: Systematists frequently differ in their interpretations of relationships. A phylogenetic classification is a hypothesis , a scientific explanation of the data and, like any hypothesis, is subject to further testing. Certain assumptions are necessary in phylogenetic classifications. A taxon should be monophyletic (all of the members of the taxon should be descendants of a single common ancestor). The characters or features used to identify the taxa must be homologous , which means that they must have a common origin, but not necessarily a common function. For example, all the parts of a flower—petals, sepals, stamens, and carpels—originate in the same way as leaves from primordia in meristems. Although they now have different functions in the flower (they're not photosynthetic), some sepals and petals structurally resemble leaves. Leaves and the parts of the flower are homologous structures. Some features that look alike do not have a common origin and are said to be analogous. An example of analogous structures is the prickles on two groups of succulent desert plants, the cacti and the euphorbs. Cacti have spines that are modified leaves; euphorbs have thorns that are modified branches. Spines and thorns look alike and are functionally similar in that both keep animals from eating the plants. Spines and thorns are analogous. This example of analogy is also an example of convergent evolution. The cactus family and the euphorb family both developed the same morphology in response to a desert environment—the cacti in North and South America, the euphorbs in Africa and Asia. The families are not related and have no recent common ancestor. Numerical taxonomy (phenetics). Systematists have tried many ways to make phyletic classifications more subjective. When computers became readily accessible in the 1960s, numerical taxonomy or phenetics became a popular approach. In practice, measurements were made of a large number of characters of a taxon, at least 60 per plant and often 100 or more. No special importance was attributed to any one of the characters. After the measurements were complete on hundreds of individuals, the data were analyzed statistically with computer programs and cluster analysis or other methods to show purported natural groupings of plants with overall similarities. Systematists' interpretations were thought to be minimized in this fashion. Cladistics. Cladistics is the most popular method of classifying organisms today. In contrast to phenetics, in which similarities are sought using as many characters as possible, cladists look for patterns using derived character states (that is, features that have evolved from an ancestral character group). The intent is to find groups of organisms that share a common ancestor and to diagram the relationship of the groups, called clades , in a cladogram (see Figure 1 ). The branching points (nodes) separate groups that have diverged in the evolutionary past from a common ancestor. All the taxa below the node lack the character state, all those above it retain it. Homologous (inherited) characters are chosen to categorize an organism and its character states. The states are hypothesized to be either ancestral or derived (evolved), and the cladogram is a test of the hypothesis.
Controversial as this change has been, shifts among groupings of the Eukarya are even more controversial, not because the data are suspect, but because biologists differ on how best to organize the new information with the old. Organisms in the five-kingdom approach of the recent past are now distributed among four kingdoms of the Domain Eukarya and the two domains of prokaryotes, Domain Bacteria and Domain Archaea. This change among groupings brings up a problem for botanists. What do you do if the organisms you study are evicted from the plant kingdom? Are you still a plant scientist if you no longer study plants? Many of the ousted groups are included in plant biology textbooks with the justification that, because the groups share many of the features of plants, it's appropriate for botanists to study them. Classifications are based on current knowledge, which is constantly changing, so rearrangements are bound to occur along with differences of opinion about what belongs where. Rarely do all parties agree. Some of the old group names survive the advent of new classification schemes and are useful ways to discuss informally some groups. Classifying Groups of Organisms Biologists use the following features of organisms to identify the major groupings of current classifications. (This book does not discuss animals and animal-like protists beyond placing them in general perspective.) Presence or absence of a defined nucleus Unicellular or multicellular with specialized organelles Mode of nutrition Presence or absence of a cell wall Composition of the cell wall Motility Mode of reproduction Kind of life cycle Nucleus The most basic division of organisms separates the living world into two groups on the basis of those possessing and those lacking a defined nucleus (plural: nuclei ). The nucleus is an organelle, which contains the major portion of the genetic material (DNA) of the cell and is surrounded by a nuclear membrane. The genetic material of Prokaryotes is not contained within a membrane-bounded nucleus. Eukaryotes all have nuclei. Cellularity The form (morphology) of an organism can be unicellular (one-celled) or multicellular (many-celled). Some unicellular organisms form filaments (strings of cells), others form sheets of cells held together by pectins, and still others form colonies that give a superficial resemblance to multicellularity. Unicellular organisms do not form tissues (similar cells organized into a functional unit) nor organs (groups of tissues organized for a particular function). Some organisms alternate a unicellular stage with a multicellular stage in their life cycles. Eukaryotic organisms have organelles , membrane-bounded structures within their cells specialized to perform certain functions. Nutrition All organisms need a source of energy to fuel their metabolism , the chemical processes that maintain life. Organisms obtain their nutrients for metabolism in one of two basic ways: 1.) Autotrophs are able to make the organic compounds they use for metabolism directly from inorganic materials; and 2.) Heterotrophs are unable to do this and obtain their nutrients from the organic materials manufactured by autotrophs. Some autotrophs are photoautotrophs. They use radiant energy from the sun in the process of photosynthesis to manufacture organic compounds. Chemoautotrophs use chemical energy in chemosynthesis , oxidizing inorganic compounds to manufacture organic nutrients. Chloroplasts are present in the photoautotrophs, absent in the chemoautotrophs. Animals are heterotrophs; they ingest (swallow) their food and then digest it internally. Fungi are heterotrophs, which release digestive enzymes into their surroundings and then absorb the nutrients into their cells. Many protists use phagotrophy , a type of nutrition in which single cells ingest food particles. Some fungi (and other organisms) are saprophages , heterotrophs that break down the organic materials of dead organisms.
Cell wall Animals and the animal-like protists have no cell walls, but most other organisms (with a few exceptions) have some kind of wall made from a variety of materials. Almost all of the prokaryote cells have walls, and a major distinction between the Bacteria and the Archaea is the presence of peptidoglycans (glycoprotein polymers) in the Bacteria and their absence in the Archaea cell walls. Fungi cell walls are made of chitin , the substance that makes the exoskeletons of lobsters, crabs, cockroaches, and other arthropods hard. The basic material of plant cells (and those of many algae) is cellulose. Lignin, suberin, waxes , and many other substances may be deposited additionally. Motility Plants in general and some animals don't move around; they are sessile (attached) to a substrate. But, many plant and sessile animal cells are motile , and they move using a variety of techniques. There are motile organisms in all of the kingdoms, so motility per se does not distinguish groups, but the kind and location of the devices employed for movement do determine groups. The organelle that propels most cells is the flagellum (plural: flagella ) or, in the terminology of some biologists, the undulipodium (plural: undulipodia ). A smaller, shorter flagellum is a cilium (plural: cilia ). The flagella are long threads of protoplasm that extend outside of the cell and have the capability for limited movement. The prokaryotes have a single-fiber flagellum that rotates; the flagella of eukaryotes are bundles that consist of nine pairs of microtubules wrapped around a central pair (a 9 + 2 configuration). A sliding action moves the microtubules. Type of reproduction Reproduction is the creation of new individuals from existing ones and can be either asexual —without special sex cells ( gametes )— or sexual , in which gametes fuse to produce new individuals. Gametes are usually haploid (with a single set of chromosomes) and their fusion ( fertilization ) results in a diploid (with two sets of chromosomes) zygote (the cell formed by the fusion of two gametes). Variations of both sexual and asexual reproduction are legion throughout the living world. Asexual reproduction occurs in some members of all the kingdoms, whereas sexual reproduction is present in all but the Archaea. Many types of asexual reproduction exist. Fission , a splitting in two of the cell, is one type of asexual reproduction. In prokaryotes, division of the genetic material accompanies fission, whereas it does not accompany fission in the eukaryotes. Yeasts and some other organisms bud , simply by pushing out and breaking off pieces of the cell. Spore-formation is a widespread method of asexual reproduction in which single-celled spores , formed in specialized structures called sporangia , are produced in large numbers. They may undergo a resting stage first, or produce new individuals directly. Sexual spores are produced in some organisms. (See Figure 1 .) Figure 1 Life cycle Three basic types of life cycles differentiate major groups of organisms (see Figure 2 ). All are variations on a general theme in which haploid cells alternate with diploid in the stages of the life cycle. Thus, meiotic (reduction) cell divisions alternate with fertilization (fusion of gametes). The three life cycles are:
