The Diversity of Life Chapter 18 The Diversity of Life, Domain IV, Part A is an introduction to biological classification. Remember, these reviews are not comprehensive; they are intended to refresh your memory and illustrate some pedagogy that will help you begin the process of becoming a teacher. More in-depth discussions of all topics covered in the review sessions may be found within the BioEd Online website. Image References: http://www.ars.usda.gov/is/graphics/photos/index.html USDA Agricultural Research Service Dairy cow by Keith Weller Seedless Grapes by Bob Nichols Leaf Beetle by Bob Richards APHS Chapter 18

Finding Order in Diversity Tacitus bellus Finding Order in Diversity To study the diversity of life, biologists use a classification system to name organisms and group them in a logical manner. Taxonomy is the branch of biology that groups and names organisms based on studies of their different characteristics. Biologists who study taxonomy are called taxonomists. Classification systems change with expanding knowledge. Populus tremuloides Quaking Aspen

Carolus von Linnaeus (1707-1778) Carolus Linnaeus Swedish botanist Developed Binomial Nomenclature Two-word naming system Genus Noun, Capitalized, Underlined or Italicized Species Descriptive, Lower Case, Underlined or Italicized Each species is assigned a two-part scientific name Ex. Ursus arctos In 1735, Carolus Linnaeus published the first edition of his Systema Naturae, which set forth his system for classifying all living things.  It has since been continually revised and expanded.

System of Classification Linnaeus’s hierarchical system of classification includes seven levels (from largest to smallest) Grizzly Bear (common name) Kingdom Animalia Phylum Chordata Class Mammalia Order Carnivora Family Ursidae Genus Ursus Species arctos Ursus arctos (scientific name) Each of the levels is called a TAXON

System of Classification K P C O F G S System of Classification Taxonomic categories, an acronym: Kingdom King Phylum Phillip Class Came Order Over Family For Genus Good Species Soup Hierarchical Classification Carolus von Linnaeus created a hierarchical classification system using seven taxonomic categories, or taxa (Kingdom, Phylum, Class, Order, Family, Genus, Species). These categories are based on shared physical characteristics, or phenotypes, within each group. Beginning with kingdom, each successive level of classification becomes more and more specific. Organisms within the same order have more in common with one another than organisms within the same class. For example, all species of bears are mammals, but not all mammals are bears. A useful pneumonic tool to help students remember the hierarchical classification system is: “King Phillip Came Over For Green Soup,” with the first letter of each word representing each category, beginning with kingdom and ending with species. References: Campbell, Neil E. and Reece, Jane B. 2002. Biology, Sixth Ed. Benjamin Cummings.

Evolutionary Classification Phylogeny – evolutionary relationships among organisms Evolutionary classification – strategy of grouping organisms together based on their evolutionary history Fossil record Comparative homologies Comparative sequencing of DNA/RNA among organisms Molecular clocks

Phylogenetic Tree Taxonomic Diagrams Mammals Turtles Lizards and Snakes Crocodiles Birds Taxonomic Diagrams Sometimes, biologists group organisms into categories that represent common ancestries, not just physical similarities. Early naturalists used physical characteristics and later, fossil data, attempting to represent evolutionary relationships among organisms. Today, modern classification systems use fossil data, physical characteristics and DNA/RNA information to draw increasingly more accurate branching diagrams. Phylogenetic trees, or phylogenies, represent hypothesized evolutionary relationships among organisms and may include extinct as well as modern species. Cladograms are based only on characteristics observable in existing species. The branching patterns in a cladogram are defined by the presence of unique, evolving innovations (derived characteristics) shared by all members of the group. References Campbell, Neil E. and Reece, Jane B. 2002. Biology, Sixth Edition. Benjamin Cummings. Judd, W.S., Campbell, C.S., Kellogg, E.S., Stevens, P.F., Monoghue, M.J. 2002. Plant Systematics: A Phylogenetic Approach, Second Edition. Sinauer Assoicates, Inc. Image References: Buffalo (Jack Dykinga), Alligator (USDA), Turkey (Scott Bauer) http://www.ars.usda.gov/is/index.html From USDA Agricultural Research Service Turtle, Snake Art Explosion, Volume 2 Clip Art Represent hypothesized evolutionary relationships

Cladogram Taxonomic Diagrams Mammals Turtles Lizards and Snakes Crocodiles Birds Attempt to trace the process of evolution by focusing on shared features

Dichotomous Keys Identify Organisms Dichotomous keys contain pairs of contrasting descriptions. After each description, the key directs the user to another pair of descriptions or identifies the organism. Example: 1. a) Is the leaf simple? Go to 2 b) Is the leaf compound? Go to 3 2. a) Are margins of the leaf jagged? Go to 4 b) Are margins of the leaf smooth? Go to 5 Dichotomous Keys of Identify Organisms Identification is the process of finding the named group to which an organism belongs. Dichotomous keys are useful tools to help identify different organisms and usually are found in field guides. Identification in the field is based on features that are observable to the eye; therefore, it is important to remember that a key is an identification tool and is not synonymous with phylogenetic diagrams, which communicate hypothesized evolutionary history. Dichotomous keys are constructed of contrasting pairs of statements. To use a dichotomous key, begin with the first pair of statements and follow the directions at the end of each statement until you reach the name of the organism you are trying to identify. With each new organism, always start at the beginning of the key (1a and 1b). The ability to use dichotomous keys is an important skill and should be incorporated into instruction throughout the year. It is important to note that when constructing a dichotomous key, each pair of contrasting descriptions must deal with the same characteristic. For example the margin of the leaf might be used for the first pair of descriptors, and the shape of the leaf might be used for another pair. An incorrect pair of statements might be: 1a) Is the leaf heart shaped? 1b) Are the edges lobed? References: Campbell, Neil E. and Reece, Jane B. 2002. Biology, Sixth Ed. Benjamin Cummings.

Domains Most inclusive category Larger than a kingdom There are 3 Eukarya – includes the kingdoms Protists, Fungi, Plants & Animals Bacteria – corresponds to the kingdom Eubacteria Archaea – corresponds to the kingdom Archaebacteria

Kingdoms Monera (Eubacteria and Archaebacteria) - Prokaryotes, with or without peptidoglycan in cell walls Protista – Eukaryotes, diverse, not fungi, plants, or animals Fungi – Eukaryotes, multicellular (except yeasts), heterotrophic, chitin in cell walls Plantae – Eukaryotes, multicellular, autotrophic, cell wall containing cellulose Animalia – Eukaryotes, multicellular, heterotrophic, no cell wall Introduction to Phylogenetic Kingdoms In our previous discussion about phylogenetic classification, we introduced classifying organisms under a broad three-domain system versus classifying organisms using a five, six, or more kingdom approach. For the purpose of this discussion, we will refer to the traditional five-kingdom system. Organisms are divided into each of five kingdoms based on defining characteristics, such as: cell type; cell structures; whether the organism is unicellular, multicellular, or has both forms; and nutrition. As new information is gathered, classifying approaches are constantly being refined. References: Margulis, L. An Illustrated Guide to the Phyla of Life on Earth. New York: W. H. Freeman & Co. 3rd edition. 1998. Whittaker, R.H. On the Broad Classification of Organisms. Quarterly Review of Biology. 34:210-226. 1959.

Kingdom Monera - Eubacteria Streptococcus mutans (can cause endocarditis and dental caries) Common name: Bacteria Unicellular prokaryotes Peptidogylcan in cell wall Ecologically diverse Basic shapes are cocci, bacilli, spirilla Reproduce both sexually and asexually endocarditis - an infection of the lining of the heart. dental caries - disease of the teeth resulting in damage to tooth structure The Kingdom Monera- Eubacteria Bacteria are the most numerous and ancient life forms found on Earth. They can live in places normally found inhospitable to other organisms (too cold, too dark, too hot, etc.). Bacteria are unicellular organisms that do not contain a nucleus or internal compartments, and their genome does not contain introns. Most species of bacteria can be assigned to two groups, based on the amount of peptidoglycan found in their cell walls. Bacteria with a thick layer of peptidoglycan in their cell walls are called “gram-positive” because they retain a blue color after staining (following a technique developed by Christian Gram.) Bacteria with a thin layer of peptidoglycan sandwiched between other layers stain orange-red following the same procedure and are called “gram-negative.” The three most common shapes of bacteria are spherical (cocci), rod (bacilli), and helices (spirilla). The number of ways that bacteria can obtain nutrition and respire contributes to their ability to inhabit so many diverse places on Earth. To obtain energy and carbon, bacteria can be photoautotrophic– harness light energy to drive metabolic processes and use CO2 as a carbon source, while others are chemoautotrophic– oxidize inorganic substances for energy and use CO2 as a carbon source, photoheterotrophic– use light to generate energy but obtain carbon from other organic molecules, or chemoheterotrophic– consume organic molecules for both energy and carbon. The chemoheterotrophs include saprobes, decomposers that absorb their nutrients from the body fluids of living hosts. Bacteria also form many diverse symbiotic relationships with other organisms. Bacteria exhibit wide variation in their use of oxygen and can be classified based on their dependence upon it. Obligate aerobes must have oxygen for cellular respiration; facultative anaerobes use oxygen if it is present, but also can grow by fermentation in an anaerobic environment. Obligate anaerobes can not tolerate oxygen at any level. Bacterial reproduction normally occurs asexually by binary fission. Bacteria do have the ability to transfer genes or segments of genes, and they do so using three mechanisms: conjugation, transformation and transduction. Conjugation involves the direct transfer of genetic material between prokaryotes. In transformation, the cells absorb fragments of DNA from the surrounding environment (even from other species). Transduction occurs when bacterial viruses play a role in transferring genetic material between prokaryotes. These abilities, along with a rapid reproductive rate, leaves little surprise as to why bacteria are “masters” of change and adaptation. Reference: Alcomo, A.I. Microbes and Society: An Introduction to Microbiology. Boston: Jones and Bartlett Publications. 2003. Image Reference: http://phil.cdc.gov/Phil/results Bacillus anthracis (spores can live in soil for years)

Kingdom Monera - Archaebacteria Cell wall does not contain peptidogylcan Cell membrane contains unusual lipids not found in other organisms Live in extreme environments (devoid of oxygen): volcanic hot springs brine pools black organic mud Archaea first detected in extreme environments, such as volcanic hot springs. The Brine Pool is a crater-like depression on the seafloor filled with very concentrated brines coming from the Luann Salt Layer. The brine contains a high concentration of methane gas that supports a surrounding dense mussel bed. The Kingdom Monera- Archaebacteria A research team led by Carl Woese at the University of Illinois, first recognized the distinction between bacteria and archaea, also known as archaebacteria. By analyzing RNA in subunits of ribosomes, they defined the early branching of the prokaryotes into Archaea and Eubacteria. In addition to their unique composition of ribosomal RNA, archaea also are distinguished by the lack of peptidoglycan in their cell walls and their unusual membrane lipids not found in other organisms. Unlike traditional bacteria, archaebacterial genes contain introns similar to those found in eukaryotes. Archaea live in the most extreme or harsh environments on Earth and are classified based on the environment in which they can be found. Methanogens produce energy from organic compounds in the presence of carbon dioxide, nitrogen and water. They produce methane and can not live in an oxygen-containing environment. Thermophiles live in very hot water found in areas around hot springs and ocean hydrothermal vents, and Halophiles are found in water with a high saline content, like the Great Salt Lake in Utah. References: Woese, C.R., Stackebrandt, E., Macke, T.J., Fox, G.E. A phylogenetic definition of the major eubacterial taxa. Systematic Applied Microbiology. 1985;6:143-51

Kingdom Protista A classification problem – consists of organisms that cannot be classified as animals, plants, or fungi Most unicellular, some colonial and some multicellular Autotrophic and heterotrophic Some move with flagella, pseudopods or cilia Animal-like, plant-like and fungus-like groups Reproduce by mitosis and meiosis Entamoeba histolytica Entamoeba histolytica - live in the host's large intestine, often via food or water contaminated with human fecal material, gastrointestinal upsets, including diarrhea The Kingdom Protista or Protoctista Members of the microbial kingdom Protista originally were defined by structure (mainly unicellular eukaryotes) and by the difficulty to classify them as either plant, fungi or animal. More recently, the concept of protists was expanded to include certain multicellular organisms such as kelp (Copeland, 1956). Thus defined, members of Protoctista range from microscopic one-celled organisms like dinoflagellates, to multicellular organisms, like seaweed. To untangle this confusing kingdom, biologists now are turning to molecular analysis. When following the traditional five- or six-kingdom classification, the Protist group contains all eukaryotes that are not fungi, plants or animals. There are unicellular, colonial, and multicellular forms, some of which show cell specialization. Protists groups include both autotrophs and heterotrophs, some of which function as detrivores. Animal-like groups are often referred to as Protozoans. The term Protozoa dates back to when members of this group were considered “first animals.” Plant-like forms are generally called algae. Traits such as method of motility, presence or absence of a shell, manner of obtaining nutrition, and reproducing, are used to categorize and discuss this diverse group, but it is important to remember that these traits do not necessarily reflect evolutionary history. Recent work suggests that green and red algae are more closely allied with land plants, and that slime molds are more closely allied to animals (Baldauf, et al. 2000). References: Baldauf, S.L., Roger, A.J., Wenk-Siefert, I., Doolittle, W.F. A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data. Science. Vol 290, November, 2000. Copeland, H. The Classification of Lower Organisms. Pacific Books: Palo Alto, CA. 1956. Margulis, L. An Illustrated Guide to the Phyla of Life on Earth. New York: W. H. Freeman & Co. 3rd edition. 1998. Image Reference: http://phil.cdc.gov/Phil/results

Kingdom Fungi Boletus zelleri (Edible, but often infected with fly larvae) Most feed on dead of decaying organic matter by secreting digestive enzymes into their food source then absorbing it into their bodies Cell walls of chitin Most multicellular; some unicellular Heterotrophic Epidermophyton floccosum (one of the causes of athlete's foot) Entamoeba histolytica - live in the host's large intestine, often via food or water contaminated with human fecal material, gastrointestinal upsets, including diarrhea The Kingdom Protista or Protoctista Members of the microbial kingdom Protista originally were defined by structure (mainly unicellular eukaryotes) and by the difficulty to classify them as either plant, fungi or animal. More recently, the concept of protists was expanded to include certain multicellular organisms such as kelp (Copeland, 1956). Thus defined, members of Protoctista range from microscopic one-celled organisms like dinoflagellates, to multicellular organisms, like seaweed. To untangle this confusing kingdom, biologists now are turning to molecular analysis. When following the traditional five- or six-kingdom classification, the Protist group contains all eukaryotes that are not fungi, plants or animals. There are unicellular, colonial, and multicellular forms, some of which show cell specialization. Protists groups include both autotrophs and heterotrophs, some of which function as detrivores. Animal-like groups are often referred to as Protozoans. The term Protozoa dates back to when members of this group were considered “first animals.” Plant-like forms are generally called algae. Traits such as method of motility, presence or absence of a shell, manner of obtaining nutrition, and reproducing, are used to categorize and discuss this diverse group, but it is important to remember that these traits do not necessarily reflect evolutionary history. Recent work suggests that green and red algae are more closely allied with land plants, and that slime molds are more closely allied to animals (Baldauf, et al. 2000). References: Baldauf, S.L., Roger, A.J., Wenk-Siefert, I., Doolittle, W.F. A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data. Science. Vol 290, November, 2000. Copeland, H. The Classification of Lower Organisms. Pacific Books: Palo Alto, CA. 1956. Margulis, L. An Illustrated Guide to the Phyla of Life on Earth. New York: W. H. Freeman & Co. 3rd edition. 1998. Image Reference: http://phil.cdc.gov/Phil/results

Sunflowers in Fargo, North Dakota Kingdom Plantae Multicellular Nonmotile – cannot move from place to place Cell wall with cellulose Mostly photosynthetic autotrophs Ginkgo biloba Ginkgos are often very long-lived. Some specimens are thought to be more than 3,500 years old. The Kingdom Plantae In the five-kingdom classification system, Plantae refers to green plants, excluding the green algae. The Kingdom Plantae includes the mosses, seed ferns, conifers, flowering plants and related groups. Plants are multicellular organisms that develop from embryos. Plants have cellulose in their cell walls that gives strength and structural support, and use chlorophyll a and b to transfer energy from the sun to chemical energy, a process called photosynthesis. In the life cycle of plants, the two multicellular body forms, the gametophyte (1n) and sporophyte (2n), alternate. The predominant form and pattern of this cycle is a key characteristic of differing plant groups. Plants are adapted primarily for life on land and have had to overcome problems of water loss and transport. Various groups of plants approach the problem of reproduction, support and transport with ingenious adaptations of vascular tissue, roots, stems, leaves, pollen, seeds, fruits, and flowers. References Judd, W., Campbell, C., Kellogg, E., Stevens, P., Donoghue, M. Plant Systematics, A Phylogenetic Approach. Massachusetts: Sinauer Associates, Inc. 2nd edition. 2002. Margulis, L. An Illustrated Guide to the Phyla of Life on Earth. New York: W. H. Freeman & Co. 3rd edition. 1998. Image Reference http://www.ars.usda.gov/is/index.html Bruce Fritz USDA Agriculture Research Service website

Hymenoptera Dialictus zephrum Kingdom Animalia Multicellular Heterotrophic No cell walls or chloroplasts Incredible diversity Txodes scapularis Deer tick Colony of sponges Invertebrate Animals Sponges have specialized cells that allow them to digest and reproduce sexually. They are sessile (non-motile) as adults but have a larval form that is able to swim. Of all the animals, sponges least have the appearance of an “animal” and for a long time were classified with plants. Cnidarians (sea anemones, jellyfish, coral, sea fans, and hydra) are mostly marine organisms. Many are characterized by special “stinging cells.” They have two body forms, the medusa and polyp. The worms include the flatworms (planaria, tapeworms, flukes), roundworms (hookworms, Trichinella) and segmented worms (earthworm, polychetes). In general worms have long tubular bodies. Many forms of worms are free-living but others are parasitic. The roundworms are the first group to exhibit a “mouth to anus” digestive system. The Annelids are segmented and have a true coelom (body cavity), and exhibit organ systems. The mollusks have a soft body and ,usually, either an internal or external shell. This group includes Bivalves (clams, oysters), Gastropods (snails, slugs), and Cephalopods (octopuses, squid, nautilus). Mollusks have a visceral mass, mantle, foot, and most respire with gills. Arthropods are found in almost all habitats in our biosphere, and they are the most numerous and successful of all members of the Animalia phyla. Arthropods have jointed appendages, an exoskeleton, and a segmented body plan. They are usually classified by structure and number of body segments and appendages. Chelicerates (spiders and scorpions), Crustaceans (shrimp, barnacles, crayfish), and Uniramians (insects, ticks, mites) are the major groups within this phylum. Echinoderms (star fish, sea urchins, sand dollars) have pentaradial symmetry, spiny skin, and a water vascular system. References: Campbell, Neil E. and Reece, Jane B. Biology, Sixth Ed. Benjamin Cummings. 2002. Image References: Art Explosion, Volume 2 Clip Art Chambered Nautilus

Hierarchical System of Classification Domain Kingdom Phylum Class Order Family Genus Species From general to more specific

How Many Kingdoms? 6 Kingdoms