BIOLOGICAL DIVERSITY: NONVASCULAR PLANTS AND NONSEED VASCULAR PLANTS
The plant kingdom contains multicellular phototrophs that usually live on land. The earliest plant fossils are from terrestrial deposits, although some plants have since returned to the water. All plant cells have a cell wall containing the carbohydrate cellulose, and often have plastids in their cytoplasm. The plant life cycle has an alternation between haploid (gametophyte) and diploid (sporophyte) generations. There are more than 300,000 living species of plants known, as well as an extensive fossil record.
Plants divide into two groups: plants lacking lignin-impregnated conducting cells (the nonvascular plants) and those containing lignin-impregnated conducting cells (the vascular plants). Living groups of nonvascular plants include the bryophytes: liverworts, hornworts, and mosses. Vascular plants are the more common plants like pines, ferns, corn, and oaks. The phylogenetic relationships within the plant kingdom are shown in Figure 1.
Evolution of Plants
Fossil and biochemical evidence indicates plants are descended from multicellular green algae. Various green algal groups have been proposed for this ancestral type, with the Charophytes often being prominently mentioned. Cladistic studies support the inclusion of the Charophytes (including the taxonomic order Coleochaetales) as sister taxa to the land plants. Algae dominated the oceans of the precambrian time over 700 million years ago. Between 500 and 400 million years ago, some algae made the transition to land, becoming plants by developing a series of adaptations to help them survive out of the water.
Vascular plants appeared by 350 million years ago, with forests soon following by 300 million years ago. Seed plants next evolved, with flowering plants appearing around 140 million years ago
The Plant Life Cycle
Plants have an alternation of generations: the diploid spore-producing plant (sporophyte) alternates with the haploid gamete-producing plant (gametophyte), as shown in Figure 3. Animal life cycles have meiosis followed immediately by gametogenesis. Gametes are produced directly by meiosis. Male gametes are sperm. Female gametes are eggs or ova.
The plant life cycle has mitosis occurring in spores, produced by meiosis, that germinate into the gametophyte phase. Gametophyte size ranges from three cells (in pollen) to several million (in a "lower plant" such as moss). Alternation of generations occurs in plants, where the sporophyte phase is succeeded by the gametophyte phase. The sporophyte phase produces spores by meiosis within a sporangium. The gametophyte phase produces gametes by mitosis within an antheridium (producing sperm) and/or archegonium (producing eggs). These different stages of the flowering plant life cycle are shown in Figure 4. Within the plant kingdom the dominance of phases varies. Nonvascular plants, the mosses and liverworts, have the gametophyte phase dominant. Vascular plants show a progression of increasing sporophyte dominance from the ferns and "fern allies" to angiosperms.
Homospory and Heterospory
Plants have two further variations on their life cycles. Plants that produce bisexual gametophytes have those gametophytes germinate from isospores (iso=same) that are about all the same size. This state is referred to as homospory (sometimes referred to as isospory). A generalized homosporous plant life cycle is shown in Figure 5. Homosporous plants produce bisexual gametophytes. Ferns are a classic example of a homosporous plant.
Plants that produce separate male and female gametophytes have those gametophytes germinate from (or within in the case of the more advanced plants) spores of different sizes (heterospores; hetero=different). The male gametophyte produces sperm, and is associated with smaller or microspores. The female gametophyte is associated with the larger or megaspores. Heterospory is considered by botanists as a significant step toward the development of the seed. A generalized heterosporous life cycle is shown in Figure 6.
Plant Adaptations to Life on Land
Organisms in water do not face many of the challenges that terrestrial creatures do. Water supports the organism, the moist surface of the creature is a superb surface for gas exchange, etc. For organisms to exist on land, a variety of challenges must be met.
1. Drying out. Once removed from water and exposed to air, organisms must deal with the need to conserve water. A number of approaches have developed, such as the development of waterproof skin (in animals), living in very moist environments (amphibians, bryophytes), and production of a waterproof surface (the cuticle in plants, cork layers and bark in woody trees).
2. Gas exchange. Organisms that live in water are often able to exchange carbon dioxide and oxygen gases through their surfaces. These exchange surfaces are moist, thin layers across which diffusion can occur. Organismal response to the challenge of drying out tends to make these surfaces thicker, waterproof, and to retard gas exchange. Consequently, another method of gas exchange must be modified or developed. Many fish already had gills and swim bladders, so when some of them began moving between ponds, the swim bladder (a gas retention structure helping buoyancy in the fish) began to act as a gas exchange surface, ultimately evolving into the terrestrial lung. Many arthropods had gills or other internal respiratory surfaces that were modified to facilitate gas exchange on land. Plants are thought to share common ancestry with algae. The plant solution to gas exchange is a new structure, the guard cells that flank openings (stomata) in the above ground parts of the plant. By opening these guard cells the plant is able to allow gas exchange by diffusion through the open stomata.
3. Support. Organisms living in water are supported by the dense liquid they live in. Once on land, the organisms had to deal with the less dense air, which could not support their weight. Adaptations to this include animal skeletons and specialized plant cells/tissues that support the plant.
4. Conduction. Single celled organisms only have tyo move materials in, out, and within their cells. A multicellular creature must do this at each cell in the body, plus move material in, out, and within the organism. Adaptations to this include the circulatory systems of animals, and the specialized conducting tissues xylem and phloem in plants. Some multicellular algae and bryophytes also have specialized conducting cells.
5. Reproduction. Organisms in water can release their gametes into the water, where the gametes will swim by flagella until they ecounter each other and fertilization happens. On land, such a scenario is not possible. Land animals have had to develop specialized reproductive systems involving fertilization when they return to water (amphibians), or internal fertilization and an amniotic egg (reptiles, birds, and mammals). Insects developed similar mechanisms. Plants have also had to deal with this, either by living in moist environments like the ferns and bryophytes do, or by developing specialized delivery systems like pollen tubes to get the sperm cells to the egg.
Bryophytes
Bryophytes are small, nonvascular plants that first evolved approximately 500 million years ago. The earliest land plants were most likely bryophytes. Bryophytes lack vascular tissue and have life cycles dominated by the gametophyte phase, as shown in Figure 7. The lack of conducting cells limits the size of the plants, generally keeping them under 5 inches high. Roots are absent in bryophytes, instead there are root-like structures known as rhizoids. Bryophytes include the hornworts, liverworts, and mosses.
Tracheophytes: The Vascular Plants
The vascular plants have specialized transporting cells xylem (for transporting water and mineral nutrients) and phloem (for transporting sugars from leaves to the rest of the plant). When we think of plants we invariably picture vascular plants. Vascular plants tend to be larger and more complex than bryophytes, and have a life cycle where the sporophyte is more prominent than the gametophyte. Vascular plants also demonstrate increased levels of organization by having organs and organ systems. The novel features oif the vascular plants are summarized in Table 2.
Vascular Plant Groups
Vascular plants first developed during the Silurian Period, about 400 million years ago. The earliest vascular plants had no roots, leaves, fruits, or flowers, and reproduced by producing spores.
Cooksonia, shown in Figure 8, is a typical early vascular plant. It was less than 15 cm tall, with stems that dichotomously branched. Dichotomous branching (where the stem divides into two ewqual branches) appears a primitive or ancestral trait in vascular plants. Some branches terminated in sporangia that produced a single size of spore.
Many scientists now consider "Cooksonia" an evolutionary grade rather than a true monophyletic taxon. Their main argument is that not all stems of Cooksonia-type plants have vascular tissue. The evolutionary situation of a grade would have some members of the group having the trait, others not. The shapes of sporangia on various specimens of Cooksonia also vary considerably.
Rhynia, shown in Figure 9, is another early vascular plant. Like Cooksonia, it lacked leaves and roots. One of the species formerly assigned to this genus, R. major, has since been reclassified as Aglaophyton major. Some paleobotanists consider A. major (Figure 10) a bryophyte, however, it does have a separate free-living sporophyte that is more prominent than the sporophyte, but appears to lack lignified conducting cells. The remaining species, R. gwynne-vaughanii is an undoubted vascular plant.
Devonian plant lines included the trimerophytes and zosterophyllophytes, which have been interpreted as related to ferns and lycophytes.
The Psilophytes
The Division Psilophyta consists of Psilotum nudum (the whisk fern, shown in Figure 11), a living plant that resembling what paleobotanists believe Cooksonia to have been: a naked, photosynthetic stem bearing sporangia. Also in the group is Tmesipteris, which resembles Psilotum except for its possession of smallo vascularized leaves arising on opposite sides of the stem. However, most paleobotanists doubt that Psilotum is a direct descendant of Cooksonia. Molecular studies suggest an affiliation with ferns for Psilotum. Psilotum also has three fused sporangia, termed a synangium, located on the sides of the stems (instead of the tips of stems as in Cooksonia).
The Lycophytes
The next group, the Division Lycophyta, have their sporangia organized into strobili (singular: strobilus). A strobilus is a series of sporangia and modified leaves closely grouped on a stem tip. The leaves in strobili are soft and fleshy as opposed to the hard, modified leaves in cones.
Leaves that contained vascular tissue are another major advance for this group. The presumed evolutionary pathway for the leaf is shown in Figure 12. The leaves in lycophytes, both living and fossil forms, are known as microphylls. This term does not imply any size constraint, but rather refers to the absence of a leaf gap in the vascular supply of the stem at the point where the leaf vascular trace departs. Ferns and other plants have megaphylls, leaves that produce this leaf gap.
Today there are fewer genera of lycophytes than during the group's heyday, the Paleozoic Era. Major living lycophytes include Lycopodium (commonly called the club moss [shown in Figure 13], although it is NOT a moss), Isoetes, and Selaginella (the so-called resurrection plant). Lycopodium produces isospores that germinate in the soil and produce a bisexual gametophyte. These spores are all approximately the same size. Selaginella and Isoetes are heterosporous, and thus produce two sizes of spores: small spores (termed microspores) that germinate to produce the male gametophyte; and larger spores (megaspores) that germinate to produce the female gametophyte. The production of two sizes of spores, and also making separate unisexual gametophytes, is thought an important step toward the seed. Modern lycophytes are small, herbaceous plants. Many of the prominent fossil members of this group produced large amounts of wood and were significant trees in the Carboniferous-aged coal swamps.
Selaginella is a heterosporous member of the lycophytes. Some species of this genus are able to withstand drying out by going dormant until they are rehydrated. For this reason these forms of the genus are commonly called resurrection plants. An example of this is shown in Figure 14.
Fossil Lycophytes: Baragwanathia and Drepanophycus
Baragwanathia, shown in Figure 15, is an undoubted lycophyte from the middle Silurian deposits of Australia. It has microphyllous leaves spirally attached to the stem, and sporangia clustered in some areas of the plant, although not in terminal strobili as in modern lycophytes.
Drepanophycus is a middle Devonian lycophyte from the Northern Hemisphere, also shown in Figure 15. Its features are very similar to modern lycophytes.
Lepidodendron and Sigillaria
The Lycophytes became significant elements of the world's flora during the Carboniferous time (the Mississippian and Pennsylvanian are terms used for this time span in the United States). These non-seed plants evolved into trees placed in the fossil genera Lepidodendron and Sigillaria, with heights reaching up to 40 meters and 20-30 meters respectively. Lepidodendron stems are composed of less wood (secondary xylem) that usually is found in gymnosperm and angiosperm trees.
We know much about the anatomy of these coal-age lycopods because of an odd type of preservation known as a coal ball. Coal balls can be peeled and the plants that are anatomically preserved within them laboriously studied to learn the details of cell structure of these coal age plants. Additionally, we have some exceptional petrifactions and compressions that reveal different layers of the plants' structure. Estimates place the bulk, up to 70%, of coal material as being derived from lycophytes.
Lepidodendron, pictured in Figures 16 and 17, was a heterosporous lycophyte tree common in coal swamps of the Carboniferous time. As with many large plant fossils, one rarely if ever finds the entire tree preserved intact. Consequently there are a number of fossil plant genera that are "organ taxa" and represent only the leaves (such as Lepidophylloides), reproductive structures (Lepidostrobus), stem (Lepidodendron), spores (Lycospora), and roots (Stigmaria). Lepidodendron had leaves borne spirally on branches that dichotomously forked, with roots also arising spirally from the stigmarian axes, and both small (microspores) and large (megaspores) formed in strobili (a loose type of soft cone). Lepidodendron may have attained heigths of nearly 40 meters, with trunks nearly 2 meters in diameter. The trees branched extensively and produced a large number of leaves. When these leaves fell from the branches, they left behind them the leaf scars characteristic of the genus.
Sigillaria was another arborescent lycopod, and is also common in coal-age deposits. In contrast to the spirally borne leaves of Lepidodendron, Sigillaria had leaved arranged in vertical rows along the stem.
The Sphenophyta
The Division Sphenophyta contains once dominant plants (both arborescent as well as herbaceous) in Paleozoic forests, equisetophytes are today relegated to minor roles as herbaceous plants. Today only a single genus, Equisetum, survives. The group is defined by their jointed stems, with many leaves being produced at a node, production of isospores in cones borne at the tips of stems, and spores bearing elaters (devices to aid in spore dispersal). Sporophyte features are seen in Figure 18. The gametophyte is small, bisexual, photosynthetic, and free-living. Silica concentrated in the stems give this group one of their common names: scouring rushes. These plants were reportedly used by American pioneers to scour the pots and pans. The fossil members of this group are often encountered in coal deposits of Carboniferous age in North America and Europe.
The Ferns
Ferns reproduce by spores from which the free-living bisexual gametophyte generation develops. There are 12,000 species of ferns today, placed in the Division Pteridophyta. The fossil history of ferns shows them to have been a dominant plant group during the Paleozoic Era. Most ferns have pinnate leaves, exhibiting small leaflets on a frond, as shown in Figure 19. Ferns have megaphyllous leaves, which cause a leaf gap in the vascular cylinder of the stem/rhizome, as shown in Figure 20. The first ferns also appear by the end of the Devonian. Some anatomical similarities suggest that ferns and sphenophytes may have shared a common ancestor within the trimerophytes.
The Fern Life Cycle
The fern gametophyte has both sexes present and is referred to as a prothallium. Prothallia develop from spores shed from the underside of the sporophyte leaves, Once fertilization occurs, the next generation sporophyte develops from the egg located in the prothallium.
Composite of 4 segmented diagrams of the fern life cycle. Note: to view this in its proper sequence you will need to open your browsert window as wide as possible. Images from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.
All text contents ©1995, 1999, 2000, 2001, 2003, 2004, by M.J. Farabee. Use of the text for educational purposes is encouraged.
Email: nolvyhindarto@gmail.com
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Senin, 22 Maret 2010
BIOLOGICAL DIVERSITY: CLASSIFICATION
Biological Diversity and Classification
Taxonomy is that branch of biology dealing with the identification and naming of organisms. The ancient Greek philosopher Aristotle apparently began the discussion on taxonomy. British naturalist John Ray is credited with revising the concept of naming and describing organisms. During the 1700s, Swedish botanist Carolus Linneus classified all then-known organisms into two large groups: the kingdoms Plantae and Animalia. Robert Whittaker in 1969 proposed five kingdoms: Plantae, Animalia, Fungi, Protista, and Monera. Other schemes involving an even greater number of kingdoms have lately been proposed, however most biologists employ Whittaker's five kingdoms. Recent studies suggest that three domains be employed: Archaea, Bacteria, and Eukarya.
Linneus attempted to pigeon-hole (or classify) all known species of his time (1753). Linnean hierarchical classification was based on the premise that the species was the smallest unit, and that each species (or taxon) nested within a higher category.
Linneus also developed the concept of binomial nomenclature, whereby scientists speaking and writing different languages could communicate clearly. For example Man in English is Hombre in Spanish, Herr in German, Ren in Chinese, and Homo in Latin. Linneus settled on Latin, which was the language of learned men at that time. If a scientist refers today to Homo, all scientists know what organism/taxon he or she means.
Construction of Phylogenetic Trees
Taxonomy is part of a larger division of biology known as systematics. Determination of phylogeny is a goal of systematics. This is done by the construction of phylogenetic trees, which in a sense represent evolutionary hypotheses and attempts to define monophyletic groups. To build these trees, we must have data, which comes from the characteristics used in classification. There are several methods of classification: traditional, phentic, and cladistic. They differ in how they value certain characters.
Traditional Classification
Data used in traditional systematics stresses both common ancestry (monophylesis) and the amount of divergence among groups. The traditional, dating to Linneaus view, is that birds have feathers, reptiles have scales, and mammals have hair. Using this as a major character, a classification like that above has been constructed. Fossils, evidence of past life, are not included in this classification. Since all of these groups have the amniotic egg, or a modification of it, they would be united in a larger taxon. Linneus placed each of these groups in a separate class within the Phylum Chordata. A primitive character is one present in the common ancestor and all members of the group, such as the amniotic egg. A derived character is one found only in a particular lineage within the larger group. In our example above, hair and feathers may be viewed as derived characters. A traditional view of our example group is that birds and mammals evolved from reptiles due to their unique derived characters.
Cladistics and Cladograms
Cladistics is a type of systematics developed by the late German biologist Willi Hennig, who attempted to formulate a more objective method of classifying organisms. Cladists group organisms based on the presence of shared derived characters, not the overall similarity of potential group members. In the example cited in Figure 3, the amniotic egg would be used to unite a group sharing common ancestry, since it would NOT be present in a group that was not in the lineage. The use of feathers and hair to separate birds and mammals from reptiles would NOT factor into a cladistic hypothesis, or cladogram, since these are characters unique to only one taxon in our group.
The value of cladistics lies in its capacity to generate (and provide a set of criteria for the evaluation) of multiple hypotheses (alternate cladograms) that can be evaluated with additional data. Almost always the "correct" cladogram employs the principle of parsimony, which proposes that the shortest number of steps or character state changes is most likely correct. An important question....is evolution always parsimonmious? However the ultimate answer to that question unfolds, the rigor cladistics introduces to systematics is useful in getting traditional systematists to look at their subjective classifications in a new light. On the diagram shown in Figure 5, shared derived characters are indicated as hauchers across the lines. The mammal clade (in this case represented by mouse and chimpanzee) is united by fur, the lizard, pigeon, mouse-chimp clade is united by claws or nails, etc.
Cladistic Classification
The example used above, if treated cladistically, would produce a very different classification! Note that crocodiles have more in common (in a cladistic sense) with birds than they do with other reptiles. Birds and crocs form a clade, or monophyletic group united by shared derived characters not present in the other groups. If we construct a Linnean group from this cladogram, we have a class of birds and crocodiles, a second class of lizards, snakes, and turtles, and a third class of mammals,
One of the more interesting applications of cladistics is to the question of the pandas. The giant panda was once thought to be a bear, but later its racoon-like characters caused it to be placed closer to racoons. The red (lesser) panda lives in the same areas of China as the giant panda, but has a far greater similarity with racoons,. DNA hybridization studies suggest the giant panda is in the bear clade, while the red panda is in the racoon clade. Both share a common ancestry, as indicated by shared derived characters, followed by convergent evolution of other characters. The diagram above indicates this divergence from common ancestry, and even attempts to show the time of that divergence.
Phenetics
Phenetics is a process by which taxa are clustered together based on the number of their similarities (or differences, depending on the numerical coefficient employed). Traits are measured and either converted into integers or input directly as numerical data. Theses data are then mathematically processed using an algorithm that generates a similarity (or distance as the case may be) matrix. Various graphical representations of this matrix include a phenogram, and principal coordinate plot. Phenetic classifications are plagued by problems of convergence and parallelism, but are useful in their attempt to objectify the classification process. My previous work on triprojectate pollen employed phenetics to deal with a wide array of subjective ratios or other classification methods. Convergence was a given with this group of fossil pollen produced by one or more groups of unknown extinct plants. Since monophylesis could not be established for the entire group, phenetics was use to help delineate possible monophyletic groups for eventual cladistic study.
Nomenclature
The naming of species and other taxa follows a set of rules, the International Code of Botanical Nomenclature for plants, the International Code of Zoological Nomenclature (ICZN) for animals.
Some general rules for nomenclature:
1. All taxa must belong to a higher taxonomic group. Often a newly discovered organism is the sole species in a single genus, within a single family...etc.
2. The first name to be validly and effectively published has priority. This rule has caused numerous name changes, especially with fossil organisms: Brontosaurus is invalid, and the correct name for the big sauropod dinosaur is Apatosaurus, Eohippus (the tiny "dawn horse") is invalid and should be referred to as Hyracotherium. Sometime, however, names can be conserved if a group of systematists agrees.
3. All taxa must have an author. When you see a scientific name such as Homo sapiens L, the L stands for Linneus, who first described and named that organism. Most scientists must have their names spelled out, for example Libopollis jarzenii Farabee et al. (an interesting fossil pollen type I stumbled across a very long time ago!).
The Kingdoms of Life
Linnaeus originally placed all living things into either the plant or animal kingdoms. As scientists learned more about the biology of many organisms, this constraining into two kingdoms became less and less defensible.
Evolutionary theory and the cell theory provide us with a basis for the interrelation of all living things. We also utilize Linneus' hierarchical classification system, adopting (generally) five kingdoms of living organisms. Viruses, as discussed later, are not considered living. Recent studies suggest that there might be a sixth Kingdom, the Archaea.
Monera
Monera are the only kingdom composed of prokaryotic organisms, they have a cell wall, and lack both membrane-bound organelles and multicellular forms. The Archaebacteria, the most ancient of this kingdom, are so different that they may belong to a separate kingdom. Other groups of Monera include the cyanobacteria (autotrophic) and eubacteria (heterotrophic).
Protista
The most ancient eukaryotic kingdom, protists include a variety of eukaryotic body (single-celled-colonial-multicellular?) and nutritional heterotrophic, autotrophic, and both) forms. Perhaps they are best defined as eukaryotes that are NOT fungi, animals, or plants.
Fungi
Fungi are a eukaryotic, heterotrophic, usually multicellular group having multinucleated cells enclosed in cells with cell walls. They obtain their energy by decomposing dead and dying organisms and absorbing their nutrients from those organisms. Some fungi also cause disease (yeast infections, rusts, and smuts), while others are useful in baking, brewing, as foods, drugs and sources for antibiotics.
Plantae
Plants are immobile, multicellular eukaryotes that produce their food by photosynthesis and have cells encased in cellulose cell walls. Plants are important sources of oxygen, food, and clothing/construction materials, as well as pigments, spices, dyes, and drugs.
Animalia
* Animals are multicellular, heterotrophic eukaryotes that are capable of mobility at some stage during their lives, and that have cells lacking cell walls. Animals provide food,
Text ©1998, 2000, 2001, 2002, by M.J. Farabee, all rights reserved. Use for educational purposes is encouraged.
Email: nolvyhindarto@gmail.com
Taxonomy is that branch of biology dealing with the identification and naming of organisms. The ancient Greek philosopher Aristotle apparently began the discussion on taxonomy. British naturalist John Ray is credited with revising the concept of naming and describing organisms. During the 1700s, Swedish botanist Carolus Linneus classified all then-known organisms into two large groups: the kingdoms Plantae and Animalia. Robert Whittaker in 1969 proposed five kingdoms: Plantae, Animalia, Fungi, Protista, and Monera. Other schemes involving an even greater number of kingdoms have lately been proposed, however most biologists employ Whittaker's five kingdoms. Recent studies suggest that three domains be employed: Archaea, Bacteria, and Eukarya.
Linneus attempted to pigeon-hole (or classify) all known species of his time (1753). Linnean hierarchical classification was based on the premise that the species was the smallest unit, and that each species (or taxon) nested within a higher category.
Linneus also developed the concept of binomial nomenclature, whereby scientists speaking and writing different languages could communicate clearly. For example Man in English is Hombre in Spanish, Herr in German, Ren in Chinese, and Homo in Latin. Linneus settled on Latin, which was the language of learned men at that time. If a scientist refers today to Homo, all scientists know what organism/taxon he or she means.
Construction of Phylogenetic Trees
Taxonomy is part of a larger division of biology known as systematics. Determination of phylogeny is a goal of systematics. This is done by the construction of phylogenetic trees, which in a sense represent evolutionary hypotheses and attempts to define monophyletic groups. To build these trees, we must have data, which comes from the characteristics used in classification. There are several methods of classification: traditional, phentic, and cladistic. They differ in how they value certain characters.
Traditional Classification
Data used in traditional systematics stresses both common ancestry (monophylesis) and the amount of divergence among groups. The traditional, dating to Linneaus view, is that birds have feathers, reptiles have scales, and mammals have hair. Using this as a major character, a classification like that above has been constructed. Fossils, evidence of past life, are not included in this classification. Since all of these groups have the amniotic egg, or a modification of it, they would be united in a larger taxon. Linneus placed each of these groups in a separate class within the Phylum Chordata. A primitive character is one present in the common ancestor and all members of the group, such as the amniotic egg. A derived character is one found only in a particular lineage within the larger group. In our example above, hair and feathers may be viewed as derived characters. A traditional view of our example group is that birds and mammals evolved from reptiles due to their unique derived characters.
Cladistics and Cladograms
Cladistics is a type of systematics developed by the late German biologist Willi Hennig, who attempted to formulate a more objective method of classifying organisms. Cladists group organisms based on the presence of shared derived characters, not the overall similarity of potential group members. In the example cited in Figure 3, the amniotic egg would be used to unite a group sharing common ancestry, since it would NOT be present in a group that was not in the lineage. The use of feathers and hair to separate birds and mammals from reptiles would NOT factor into a cladistic hypothesis, or cladogram, since these are characters unique to only one taxon in our group.
The value of cladistics lies in its capacity to generate (and provide a set of criteria for the evaluation) of multiple hypotheses (alternate cladograms) that can be evaluated with additional data. Almost always the "correct" cladogram employs the principle of parsimony, which proposes that the shortest number of steps or character state changes is most likely correct. An important question....is evolution always parsimonmious? However the ultimate answer to that question unfolds, the rigor cladistics introduces to systematics is useful in getting traditional systematists to look at their subjective classifications in a new light. On the diagram shown in Figure 5, shared derived characters are indicated as hauchers across the lines. The mammal clade (in this case represented by mouse and chimpanzee) is united by fur, the lizard, pigeon, mouse-chimp clade is united by claws or nails, etc.
Cladistic Classification
The example used above, if treated cladistically, would produce a very different classification! Note that crocodiles have more in common (in a cladistic sense) with birds than they do with other reptiles. Birds and crocs form a clade, or monophyletic group united by shared derived characters not present in the other groups. If we construct a Linnean group from this cladogram, we have a class of birds and crocodiles, a second class of lizards, snakes, and turtles, and a third class of mammals,
One of the more interesting applications of cladistics is to the question of the pandas. The giant panda was once thought to be a bear, but later its racoon-like characters caused it to be placed closer to racoons. The red (lesser) panda lives in the same areas of China as the giant panda, but has a far greater similarity with racoons,. DNA hybridization studies suggest the giant panda is in the bear clade, while the red panda is in the racoon clade. Both share a common ancestry, as indicated by shared derived characters, followed by convergent evolution of other characters. The diagram above indicates this divergence from common ancestry, and even attempts to show the time of that divergence.
Phenetics
Phenetics is a process by which taxa are clustered together based on the number of their similarities (or differences, depending on the numerical coefficient employed). Traits are measured and either converted into integers or input directly as numerical data. Theses data are then mathematically processed using an algorithm that generates a similarity (or distance as the case may be) matrix. Various graphical representations of this matrix include a phenogram, and principal coordinate plot. Phenetic classifications are plagued by problems of convergence and parallelism, but are useful in their attempt to objectify the classification process. My previous work on triprojectate pollen employed phenetics to deal with a wide array of subjective ratios or other classification methods. Convergence was a given with this group of fossil pollen produced by one or more groups of unknown extinct plants. Since monophylesis could not be established for the entire group, phenetics was use to help delineate possible monophyletic groups for eventual cladistic study.
Nomenclature
The naming of species and other taxa follows a set of rules, the International Code of Botanical Nomenclature for plants, the International Code of Zoological Nomenclature (ICZN) for animals.
Some general rules for nomenclature:
1. All taxa must belong to a higher taxonomic group. Often a newly discovered organism is the sole species in a single genus, within a single family...etc.
2. The first name to be validly and effectively published has priority. This rule has caused numerous name changes, especially with fossil organisms: Brontosaurus is invalid, and the correct name for the big sauropod dinosaur is Apatosaurus, Eohippus (the tiny "dawn horse") is invalid and should be referred to as Hyracotherium. Sometime, however, names can be conserved if a group of systematists agrees.
3. All taxa must have an author. When you see a scientific name such as Homo sapiens L, the L stands for Linneus, who first described and named that organism. Most scientists must have their names spelled out, for example Libopollis jarzenii Farabee et al. (an interesting fossil pollen type I stumbled across a very long time ago!).
The Kingdoms of Life
Linnaeus originally placed all living things into either the plant or animal kingdoms. As scientists learned more about the biology of many organisms, this constraining into two kingdoms became less and less defensible.
Evolutionary theory and the cell theory provide us with a basis for the interrelation of all living things. We also utilize Linneus' hierarchical classification system, adopting (generally) five kingdoms of living organisms. Viruses, as discussed later, are not considered living. Recent studies suggest that there might be a sixth Kingdom, the Archaea.
Monera
Monera are the only kingdom composed of prokaryotic organisms, they have a cell wall, and lack both membrane-bound organelles and multicellular forms. The Archaebacteria, the most ancient of this kingdom, are so different that they may belong to a separate kingdom. Other groups of Monera include the cyanobacteria (autotrophic) and eubacteria (heterotrophic).
Protista
The most ancient eukaryotic kingdom, protists include a variety of eukaryotic body (single-celled-colonial-multicellular?) and nutritional heterotrophic, autotrophic, and both) forms. Perhaps they are best defined as eukaryotes that are NOT fungi, animals, or plants.
Fungi
Fungi are a eukaryotic, heterotrophic, usually multicellular group having multinucleated cells enclosed in cells with cell walls. They obtain their energy by decomposing dead and dying organisms and absorbing their nutrients from those organisms. Some fungi also cause disease (yeast infections, rusts, and smuts), while others are useful in baking, brewing, as foods, drugs and sources for antibiotics.
Plantae
Plants are immobile, multicellular eukaryotes that produce their food by photosynthesis and have cells encased in cellulose cell walls. Plants are important sources of oxygen, food, and clothing/construction materials, as well as pigments, spices, dyes, and drugs.
Animalia
* Animals are multicellular, heterotrophic eukaryotes that are capable of mobility at some stage during their lives, and that have cells lacking cell walls. Animals provide food,
Text ©1998, 2000, 2001, 2002, by M.J. Farabee, all rights reserved. Use for educational purposes is encouraged.
Email: nolvyhindarto@gmail.com
Biological-diversity:classification
BIOLOGICAL DIVERSITY: CLASSIFICATION
Biological Diversity and Classification
Taxonomy is that branch of biology dealing with the identification and naming of organisms. The ancient Greek philosopher Aristotle apparently began the discussion on taxonomy. British naturalist John Ray is credited with revising the concept of naming and describing organisms. During the 1700s, Swedish botanist Carolus Linneus classified all then-known organisms into two large groups: the kingdoms Plantae and Animalia. Robert Whittaker in 1969 proposed five kingdoms: Plantae, Animalia, Fungi, Protista, and Monera. Other schemes involving an even greater number of kingdoms have lately been proposed, however most biologists employ Whittaker's five kingdoms. Recent studies suggest that three domains be employed: Archaea, Bacteria, and Eukarya.
Linneus attempted to pigeon-hole (or classify) all known species of his time (1753). Linnean hierarchical classification was based on the premise that the species was the smallest unit, and that each species (or taxon) nested within a higher category.
Linneus also developed the concept of binomial nomenclature, whereby scientists speaking and writing different languages could communicate clearly. For example Man in English is Hombre in Spanish, Herr in German, Ren in Chinese, and Homo in Latin. Linneus settled on Latin, which was the language of learned men at that time. If a scientist refers today to Homo, all scientists know what organism/taxon he or she means.
Construction of Phylogenetic Trees
Taxonomy is part of a larger division of biology known as systematics. Determination of phylogeny is a goal of systematics. This is done by the construction of phylogenetic trees, which in a sense represent evolutionary hypotheses and attempts to define monophyletic groups. To build these trees, we must have data, which comes from the characteristics used in classification. There are several methods of classification: traditional, phentic, and cladistic. They differ in how they value certain characters.
Traditional Classification
Data used in traditional systematics stresses both common ancestry (monophylesis) and the amount of divergence among groups. The traditional, dating to Linneaus view, is that birds have feathers, reptiles have scales, and mammals have hair. Using this as a major character, a classification like that above has been constructed. Fossils, evidence of past life, are not included in this classification. Since all of these groups have the amniotic egg, or a modification of it, they would be united in a larger taxon. Linneus placed each of these groups in a separate class within the Phylum Chordata. A primitive character is one present in the common ancestor and all members of the group, such as the amniotic egg. A derived character is one found only in a particular lineage within the larger group. In our example above, hair and feathers may be viewed as derived characters. A traditional view of our example group is that birds and mammals evolved from reptiles due to their unique derived characters.
Cladistics and Cladograms
Cladistics is a type of systematics developed by the late German biologist Willi Hennig, who attempted to formulate a more objective method of classifying organisms. Cladists group organisms based on the presence of shared derived characters, not the overall similarity of potential group members. In the example cited in Figure 3, the amniotic egg would be used to unite a group sharing common ancestry, since it would NOT be present in a group that was not in the lineage. The use of feathers and hair to separate birds and mammals from reptiles would NOT factor into a cladistic hypothesis, or cladogram, since these are characters unique to only one taxon in our group.
The value of cladistics lies in its capacity to generate (and provide a set of criteria for the evaluation) of multiple hypotheses (alternate cladograms) that can be evaluated with additional data. Almost always the "correct" cladogram employs the principle of parsimony, which proposes that the shortest number of steps or character state changes is most likely correct. An important question....is evolution always parsimonmious? However the ultimate answer to that question unfolds, the rigor cladistics introduces to systematics is useful in getting traditional systematists to look at their subjective classifications in a new light. On the diagram shown in Figure 5, shared derived characters are indicated as hauchers across the lines. The mammal clade (in this case represented by mouse and chimpanzee) is united by fur, the lizard, pigeon, mouse-chimp clade is united by claws or nails, etc.
Cladistic Classification
The example used above, if treated cladistically, would produce a very different classification! Note that crocodiles have more in common (in a cladistic sense) with birds than they do with other reptiles. Birds and crocs form a clade, or monophyletic group united by shared derived characters not present in the other groups. If we construct a Linnean group from this cladogram, we have a class of birds and crocodiles, a second class of lizards, snakes, and turtles, and a third class of mammals,
One of the more interesting applications of cladistics is to the question of the pandas. The giant panda was once thought to be a bear, but later its racoon-like characters caused it to be placed closer to racoons. The red (lesser) panda lives in the same areas of China as the giant panda, but has a far greater similarity with racoons,. DNA hybridization studies suggest the giant panda is in the bear clade, while the red panda is in the racoon clade. Both share a common ancestry, as indicated by shared derived characters, followed by convergent evolution of other characters. The diagram above indicates this divergence from common ancestry, and even attempts to show the time of that divergence.
Phenetics
Phenetics is a process by which taxa are clustered together based on the number of their similarities (or differences, depending on the numerical coefficient employed). Traits are measured and either converted into integers or input directly as numerical data. Theses data are then mathematically processed using an algorithm that generates a similarity (or distance as the case may be) matrix. Various graphical representations of this matrix include a phenogram, and principal coordinate plot. Phenetic classifications are plagued by problems of convergence and parallelism, but are useful in their attempt to objectify the classification process. My previous work on triprojectate pollen employed phenetics to deal with a wide array of subjective ratios or other classification methods. Convergence was a given with this group of fossil pollen produced by one or more groups of unknown extinct plants. Since monophylesis could not be established for the entire group, phenetics was use to help delineate possible monophyletic groups for eventual cladistic study.
Nomenclature
The naming of species and other taxa follows a set of rules, the International Code of Botanical Nomenclature for plants, the International Code of Zoological Nomenclature (ICZN) for animals.
Some general rules for nomenclature:
1. All taxa must belong to a higher taxonomic group. Often a newly discovered organism is the sole species in a single genus, within a single family...etc.
2. The first name to be validly and effectively published has priority. This rule has caused numerous name changes, especially with fossil organisms: Brontosaurus is invalid, and the correct name for the big sauropod dinosaur is Apatosaurus, Eohippus (the tiny "dawn horse") is invalid and should be referred to as Hyracotherium. Sometime, however, names can be conserved if a group of systematists agrees.
3. All taxa must have an author. When you see a scientific name such as Homo sapiens L, the L stands for Linneus, who first described and named that organism. Most scientists must have their names spelled out, for example Libopollis jarzenii Farabee et al. (an interesting fossil pollen type I stumbled across a very long time ago!).
The Kingdoms of Life
Linnaeus originally placed all living things into either the plant or animal kingdoms. As scientists learned more about the biology of many organisms, this constraining into two kingdoms became less and less defensible.
Evolutionary theory and the cell theory provide us with a basis for the interrelation of all living things. We also utilize Linneus' hierarchical classification system, adopting (generally) five kingdoms of living organisms. Viruses, as discussed later, are not considered living. Recent studies suggest that there might be a sixth Kingdom, the Archaea.
Monera
Monera are the only kingdom composed of prokaryotic organisms, they have a cell wall, and lack both membrane-bound organelles and multicellular forms. The Archaebacteria, the most ancient of this kingdom, are so different that they may belong to a separate kingdom. Other groups of Monera include the cyanobacteria (autotrophic) and eubacteria (heterotrophic).
Protista
The most ancient eukaryotic kingdom, protists include a variety of eukaryotic body (single-celled-colonial-multicellular?) and nutritional heterotrophic, autotrophic, and both) forms. Perhaps they are best defined as eukaryotes that are NOT fungi, animals, or plants.
Fungi
Fungi are a eukaryotic, heterotrophic, usually multicellular group having multinucleated cells enclosed in cells with cell walls. They obtain their energy by decomposing dead and dying organisms and absorbing their nutrients from those organisms. Some fungi also cause disease (yeast infections, rusts, and smuts), while others are useful in baking, brewing, as foods, drugs and sources for antibiotics.
Plantae
Plants are immobile, multicellular eukaryotes that produce their food by photosynthesis and have cells encased in cellulose cell walls. Plants are important sources of oxygen, food, and clothing/construction materials, as well as pigments, spices, dyes, and drugs.
Animalia
* Animals are multicellular, heterotrophic eukaryotes that are capable of mobility at some stage during their lives, and that have cells lacking cell walls. Animals provide food,
Text �1998, 2000, 2001, 2002, by M.J. Farabee, all rights reserved. Use for educational purposes is encouraged.
Email: nolvyhindarto@gmail.com
Biological Diversity and Classification
Taxonomy is that branch of biology dealing with the identification and naming of organisms. The ancient Greek philosopher Aristotle apparently began the discussion on taxonomy. British naturalist John Ray is credited with revising the concept of naming and describing organisms. During the 1700s, Swedish botanist Carolus Linneus classified all then-known organisms into two large groups: the kingdoms Plantae and Animalia. Robert Whittaker in 1969 proposed five kingdoms: Plantae, Animalia, Fungi, Protista, and Monera. Other schemes involving an even greater number of kingdoms have lately been proposed, however most biologists employ Whittaker's five kingdoms. Recent studies suggest that three domains be employed: Archaea, Bacteria, and Eukarya.
Linneus attempted to pigeon-hole (or classify) all known species of his time (1753). Linnean hierarchical classification was based on the premise that the species was the smallest unit, and that each species (or taxon) nested within a higher category.
Linneus also developed the concept of binomial nomenclature, whereby scientists speaking and writing different languages could communicate clearly. For example Man in English is Hombre in Spanish, Herr in German, Ren in Chinese, and Homo in Latin. Linneus settled on Latin, which was the language of learned men at that time. If a scientist refers today to Homo, all scientists know what organism/taxon he or she means.
Construction of Phylogenetic Trees
Taxonomy is part of a larger division of biology known as systematics. Determination of phylogeny is a goal of systematics. This is done by the construction of phylogenetic trees, which in a sense represent evolutionary hypotheses and attempts to define monophyletic groups. To build these trees, we must have data, which comes from the characteristics used in classification. There are several methods of classification: traditional, phentic, and cladistic. They differ in how they value certain characters.
Traditional Classification
Data used in traditional systematics stresses both common ancestry (monophylesis) and the amount of divergence among groups. The traditional, dating to Linneaus view, is that birds have feathers, reptiles have scales, and mammals have hair. Using this as a major character, a classification like that above has been constructed. Fossils, evidence of past life, are not included in this classification. Since all of these groups have the amniotic egg, or a modification of it, they would be united in a larger taxon. Linneus placed each of these groups in a separate class within the Phylum Chordata. A primitive character is one present in the common ancestor and all members of the group, such as the amniotic egg. A derived character is one found only in a particular lineage within the larger group. In our example above, hair and feathers may be viewed as derived characters. A traditional view of our example group is that birds and mammals evolved from reptiles due to their unique derived characters.
Cladistics and Cladograms
Cladistics is a type of systematics developed by the late German biologist Willi Hennig, who attempted to formulate a more objective method of classifying organisms. Cladists group organisms based on the presence of shared derived characters, not the overall similarity of potential group members. In the example cited in Figure 3, the amniotic egg would be used to unite a group sharing common ancestry, since it would NOT be present in a group that was not in the lineage. The use of feathers and hair to separate birds and mammals from reptiles would NOT factor into a cladistic hypothesis, or cladogram, since these are characters unique to only one taxon in our group.
The value of cladistics lies in its capacity to generate (and provide a set of criteria for the evaluation) of multiple hypotheses (alternate cladograms) that can be evaluated with additional data. Almost always the "correct" cladogram employs the principle of parsimony, which proposes that the shortest number of steps or character state changes is most likely correct. An important question....is evolution always parsimonmious? However the ultimate answer to that question unfolds, the rigor cladistics introduces to systematics is useful in getting traditional systematists to look at their subjective classifications in a new light. On the diagram shown in Figure 5, shared derived characters are indicated as hauchers across the lines. The mammal clade (in this case represented by mouse and chimpanzee) is united by fur, the lizard, pigeon, mouse-chimp clade is united by claws or nails, etc.
Cladistic Classification
The example used above, if treated cladistically, would produce a very different classification! Note that crocodiles have more in common (in a cladistic sense) with birds than they do with other reptiles. Birds and crocs form a clade, or monophyletic group united by shared derived characters not present in the other groups. If we construct a Linnean group from this cladogram, we have a class of birds and crocodiles, a second class of lizards, snakes, and turtles, and a third class of mammals,
One of the more interesting applications of cladistics is to the question of the pandas. The giant panda was once thought to be a bear, but later its racoon-like characters caused it to be placed closer to racoons. The red (lesser) panda lives in the same areas of China as the giant panda, but has a far greater similarity with racoons,. DNA hybridization studies suggest the giant panda is in the bear clade, while the red panda is in the racoon clade. Both share a common ancestry, as indicated by shared derived characters, followed by convergent evolution of other characters. The diagram above indicates this divergence from common ancestry, and even attempts to show the time of that divergence.
Phenetics
Phenetics is a process by which taxa are clustered together based on the number of their similarities (or differences, depending on the numerical coefficient employed). Traits are measured and either converted into integers or input directly as numerical data. Theses data are then mathematically processed using an algorithm that generates a similarity (or distance as the case may be) matrix. Various graphical representations of this matrix include a phenogram, and principal coordinate plot. Phenetic classifications are plagued by problems of convergence and parallelism, but are useful in their attempt to objectify the classification process. My previous work on triprojectate pollen employed phenetics to deal with a wide array of subjective ratios or other classification methods. Convergence was a given with this group of fossil pollen produced by one or more groups of unknown extinct plants. Since monophylesis could not be established for the entire group, phenetics was use to help delineate possible monophyletic groups for eventual cladistic study.
Nomenclature
The naming of species and other taxa follows a set of rules, the International Code of Botanical Nomenclature for plants, the International Code of Zoological Nomenclature (ICZN) for animals.
Some general rules for nomenclature:
1. All taxa must belong to a higher taxonomic group. Often a newly discovered organism is the sole species in a single genus, within a single family...etc.
2. The first name to be validly and effectively published has priority. This rule has caused numerous name changes, especially with fossil organisms: Brontosaurus is invalid, and the correct name for the big sauropod dinosaur is Apatosaurus, Eohippus (the tiny "dawn horse") is invalid and should be referred to as Hyracotherium. Sometime, however, names can be conserved if a group of systematists agrees.
3. All taxa must have an author. When you see a scientific name such as Homo sapiens L, the L stands for Linneus, who first described and named that organism. Most scientists must have their names spelled out, for example Libopollis jarzenii Farabee et al. (an interesting fossil pollen type I stumbled across a very long time ago!).
The Kingdoms of Life
Linnaeus originally placed all living things into either the plant or animal kingdoms. As scientists learned more about the biology of many organisms, this constraining into two kingdoms became less and less defensible.
Evolutionary theory and the cell theory provide us with a basis for the interrelation of all living things. We also utilize Linneus' hierarchical classification system, adopting (generally) five kingdoms of living organisms. Viruses, as discussed later, are not considered living. Recent studies suggest that there might be a sixth Kingdom, the Archaea.
Monera
Monera are the only kingdom composed of prokaryotic organisms, they have a cell wall, and lack both membrane-bound organelles and multicellular forms. The Archaebacteria, the most ancient of this kingdom, are so different that they may belong to a separate kingdom. Other groups of Monera include the cyanobacteria (autotrophic) and eubacteria (heterotrophic).
Protista
The most ancient eukaryotic kingdom, protists include a variety of eukaryotic body (single-celled-colonial-multicellular?) and nutritional heterotrophic, autotrophic, and both) forms. Perhaps they are best defined as eukaryotes that are NOT fungi, animals, or plants.
Fungi
Fungi are a eukaryotic, heterotrophic, usually multicellular group having multinucleated cells enclosed in cells with cell walls. They obtain their energy by decomposing dead and dying organisms and absorbing their nutrients from those organisms. Some fungi also cause disease (yeast infections, rusts, and smuts), while others are useful in baking, brewing, as foods, drugs and sources for antibiotics.
Plantae
Plants are immobile, multicellular eukaryotes that produce their food by photosynthesis and have cells encased in cellulose cell walls. Plants are important sources of oxygen, food, and clothing/construction materials, as well as pigments, spices, dyes, and drugs.
Animalia
* Animals are multicellular, heterotrophic eukaryotes that are capable of mobility at some stage during their lives, and that have cells lacking cell walls. Animals provide food,
Text �1998, 2000, 2001, 2002, by M.J. Farabee, all rights reserved. Use for educational purposes is encouraged.
Email: nolvyhindarto@gmail.com
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