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Taxonomy Unit 11: Classification (And REALLY quick survey of kingdoms) Honors Biology • Branch of biology concerned with identifying and naming organisms. • Naming and identifying organisms began with the Greeks and Romans. • Middle ages, organisms were described using long Latin descriptions. • Much later, John Ray, a British naturalist argued that each organism should have a set name. The Dichotomous Key: •device for identifying an unknown organism, set up as a sequence of choices between two (sometimes more) statements – Couplets, which are based on characteristics of the organism. •By making the correct choice, the name of the organism will be revealed. A sample dichotomous key: •couplets together 1a. Flower open with distinct petals .................................go to 2 1b. Flower neither open nor has distinct petals ......... Aquilegia 2a. Petals usually striped to tip; multiple filaments project just outside of center ….....................................Clematis 2b. Petals faint or no striping; no filaments outside of center………………………………....................................... go to 3 3a. Pollen held close to center.................................... Ranuculus 3b. Pollen on stamens away from center .....................Anemone Constructing Keys • Use constant characteristics • Use measurements • Make the choice a positive one - something "is" instead of "is not". • If possible, start the couplet with the same word. • If possible, start different couplets with different words. Using a Key The Binomial System • Always read both choices, even if the first seems to be the logical one at first. • Be sure you understand the meaning of the terms involved. When measurements are given, measure • If the choice is not clear, for whatever reason, try both divisions. If you end up with two possible answers, read descriptions of the two choices to help you decide. Linnaeus’s System of Classification • Carolus Linnaeus (1701-1778) developed a binomial system to name species. • A binomial system of nomenclature names organisms using a two-part Latin name. – First part is the genus; closely related species are assigned to the same genus. – Second part is the specific epithet; it usually provides something descriptive about an organism, its discoverer, or where it was discovered (this part is also called the species part of the name) – A scientific name consists of both genus and specific epithet (e.g., Lilium buibiferum and Lilium canadense). – Both names are italicized if in print or underlined if handwritten; the first letter of only the genus is capitalized. – The genus can be abbreviated when used with a specific epithet if the full name was given before. Classification of Ursus arctos Grizzly bear Modern biologists have added Domain above the level of Kingdom Kingdom Phylum Class Order Family Genus Species • • • • • • • King Phillip Came Over From Germany Singing Black bear Giant panda Red fox Albert squirrel Coral snake Sea star KINGDOM Animalia PHYLUM Chordata CLASS Mammalia ORDER Carnivora FAMILY Ursidae GENUS Ursus SPECIES Ursus arctos Common names • • • • vary with different languages lump many species under one name have various names for the same species same name may refer to different organisms in different regions. What is a FROGMOUTH? What is an elk? •elk, name applied to several large members of the deer family. It most properly designates the largest member of the family, Alces alces, found in the northern regions of Eurasia and North America. In North America this animal is called moose. The name elk is used in North America to designate a different animal, the wapiti, closely related to the red deer of Europe. The prehistoric Irish elk, Megaceros giganteus, is still another species, related to the fallow deer. It was found in Europe and W Asia in Pleistocene times and had an 11-ft (3.3-m) antler span, the largest of any deer. Naming • The job of naming is unfinished. – 3 - 20 million species live on Earth. – one million species of animals and a half million plant species are named – Some groups, such as birds, are nearly all known; some insect groups, bacteria, and protists are mostly unknown. – As more molecular evidence is gathered, entire phylogenetic tree branches must be moved to reflect new information What is a Fish? • Starfish? • Jellyfish? • Crayfish? What Is a Species? • Linnaeus considered each species to have a unique structure that made it distinct. – Distinguishing species on structure can be a problem because variations occur among members. – Males and females may have different forms, as well as juveniles and adults. • The biological definition of a species states a species can interbreed and share the same gene pool. • Distinguishing species on the basis of reproductive isolation can also be a problem – Some species do not reproduce sexually. – Some species hybridize. – Reproductive isolation can be difficult to observe. • When a species has a wide geographic range, variant types may tend to interbreed where they overlap; these populations may be named as subspecies. – The rat snakes Elaphe obsoleta obsoleta and Elaphe obsoleta bairdi are subspecies of Elaphe obsoleta. – Including the subspecies makes this a trinomial, or three-part, name. From the standpoint of classification: – categories are established to assign species on the basis of their relationship to other species. • Species is a taxonomic category below the rank of genus. – Species share a more recent common ancestor with species in same genus than with those in other taxa. – A taxon is a group of organisms in a classification category; Rosa or Felis are taxa at the genus level. – A common ancestor is valid if there are at least two lines of common descent Homology • Homology is a character similarity due to having a common ancestry. • Homologous structures are related to each other through common descent but may differ in structure and function (e.g., the forelimbs of a horse and the wings of a bat) – Analogous structures have the same function but are not derived from the same organ in a common ancestor (e.g., the wings of an insect and the wings of a bat). – Homology helps indicate when species belong to a related group. Example • Panda evolution – Chinese giant panda resembles a bear, has a false thumb, but bones and teeth resembled a raccoon – The red panda has similar features but lacks the false thumb – Results of DNA hybridization suggest the giant panda diverged from the bear lineage and the red panda diverged from the raccoon lineage. Classification Categories • We use eight categories (taxons) for classification: species, genus, family, order, class, phylum (or division for plants), kingdom, and domain – The higher the category, the more inclusive it is. – Members of a domain share general characters; members of a species share specific characters. • Characters are any structural, chromosomal, or molecular feature that distinguishes groups. – Additional levels of classification can be added by adding super-, sub-, or infra- (e.g., suborder). Molecular Data • Speciation occurs when mutations bring about changes in base pair sequences of DNA • Each distinct lineage accumulates changes in DNA base pair sequences and amino acid sequences in proteins over time. • Molecular changes are numerical and can sometimes sort out relationships obscured by convergence. • Advances in analyzing nucleotide and amino acid sequences make abundant data available to researchers. Cladistic Systematics • Cladistics analyzes primitive and derived characters and constructs cladograms on the basis of shared derived characters • Cladogram is a diagram showing relationships among species based on shared, derived characters. • Constructing a Cladogram – First step is to construct a table of characters of the taxa being compared. – Homologies shared by certain lineages are shared derived characters. – A clade is an evolutionary branch that includes a common ancestor and all its descendent species. Some Definitions • Classification reflects phylogeny; one goal of systematics is to create phylogenetic trees. – Systematics is the study of the diversity of organisms using information from cellular to population levels – Phylogeny is the evolutionary history of a group of organisms. – A phylogenetic tree indicates common ancestors and lines of descent. • A primitive character is a trait that is present in a common ancestor and all members of a group • An outgroup is a taxon that is outside the group of interest; it is included for comparison • A derived character is present only in a specific line of descent. – Different lineages diverging from a common ancestor may have different derived characters This simple cladogram shows primitive / derived characters • Each larger circle represents a group of primitive characters; the smaller circle are groups that share a set of derived characters Cladogram of Six Kingdoms and Three Domains DOMAIN ARCHAEA DOMAIN EUKARYA Kingdoms DOMAIN BACTERIA Eubacteria Archaebacteria Protista Plantae Fungi Animalia • Traditional Classification is based on structural similarities, without an attempt to find genetic or evolutionary relationships. Three-Domain System • Cladistics, or evolutionary classification, bases classification on derived characters, such as the molted skeleton and segmentation found in all crustaceans. Cladistics attempts to classify based on evolutionary history. The diagram produced is a cladogram. Domain Bacteria; Kingdom Eubacteria • Unicellular, prokaryotic • Cell walls – Thick, rigid, contain peptidoglycan • Autotrophic by photosythesis, or Heterotrophic • Some require oxygen (aerobic); others are killed by oxygen (anaerobic) • Examples : Escherichia coli, Mycobacterium • tuberculosis, Salmonella enteridis Domain Archaea : Kingdom Archaebacteria • Unicellular and prokaryotic • • • • Cell walls without peptidoglycan Autotroph or Heterotroph Aerobic and anaerobic forms Habitats – live in extreme environments – Arctic Ice, geysers, hot springs, brine (like the Great Salt Lake), deep ocean volcanic vents • Sequencing of rRNA suggests all organisms evolved along three distinct lineages: domains Bacteria, Archaea, and Eukarya. • Bacteria diverged first; Archaea and Eukarya are more closely related than either is to bacteria. • The archaea live in extreme environments: – methanogens in anaerobic swamps – halophiles in salt lakes – thermoacidophiles in hot acidic environments Domain Eukarya : Kingdom Protista • • • • • Eukaryotic organisms not classified as plants, animals, or fungi Most unicellular, some multicellular Cell wall with cellulose Autotrophic by photosynthesis, or Heterotrophic A miscellaneous category to put organisms that do not fit elsewhere; most likely to be revised in near future Domain Eukarya : Kingdom Fungi • Multicellular and Unicellular • Cell walls of chitin • Heterotrophic by absorption; secrete digestive enzymes into food, then absorb usable molecules • Examples : Yeast, Molds, Mushrooms Domain Eukarya : Kingdom Plantae • • • • • Domain Eukarya : Kingdom Animalia • • • • Multicellular; mostly motile No cell walls Heterotrophic by ingestion Examples: sponges, jellyfish, flatworms, earthworms, mollusks, arthropods, starfish, frogs Multicellular and nonmotile Cell walls made of cellulose Photosynthetic autotrophs Food stored as starch Examples: mosses, ferns, conifers, flowering plants • STOP 2011 Domain Bacteria In Depth Bacteria and Viruses • Bacteria occur in many shapes and sizes. Most bacteria have one of three basic shapes: rod-shaped, sphere-shaped, or spiral-shaped. • Rod-shaped bacteria are called bacilli (singular, bacillus). An example of bacilli is Escherichia coli. • Sphere-shaped bacteria are called cocci (singular, coccus). An example of cocci is Micrococcus luteus. Domain Bacteria, continued Three Bacterial Cell Shapes • Spiral shaped bacteria are called spirilla (singular, spirillum). An example of spirilla bacteria includes Spirillum volutans. • Cocci that form chains similar to a string of beads are called streptococci. • Cocci that form clusters similar to a bunch of grapes are called staphylococci. Domain Bacteria, continued Gram Staining • Gram Stain – Most species of bacteria are classified into two categories based on the structure of their cell walls as determined by a technique called the Gram stain. – Gram-positive bacteria have a thick layer of peptidoglycan in their cell wall, and they appear purple under a microscope after the Gram-staining procedure. – Gram-negative bacteria have a thin layer of peptidoglycan in their cell wall, and they appear reddish-pink under a microscope after the Gramstaining procedure. Gram Stain Click below to watch the Visual Concept. Important Bacterial Groups • Bacteria are also classified by their biochemical properties and evolutionary relationships. • Proteobacteria Visual Concept – Proteobacteria are one of the largest and most diverse groups of bacteria, and contain several subgroups that are extremely diverse. – Members of this group include bacteria of the genus Rhizobium, the genus Agrobacterium, and the bacterium Escherichia coli. Important Bacterial Groups, continued • Gram-Positive Bacteria – Not all of the bacteria in this group are Gram-positive. Biologists place a few species of Gram-negative bacteria in this group because these species are genetically similar to Gram-positive bacteria. – Members of this group include the streptococcal species, Clostridium botulinum, Bacillus anthracis, and members of the genus Mycobacteria. Important Bacterial Groups, continued Important Bacterial Groups, continued • Gram-Positive Bacteria, continued – Actinomycetes are Gram-positive bacteria, some species of which produce antibiotics. • Antibiotics are chemicals that inhibit the growth of or kill other bacteria. Streptomycin and tetracycline are examples of antibiotics that are used medicinally. Important Bacterial Groups, continued • Spirochetes • Cyanobacteria – Cyanobacteria use photosynthesis to get energy from sunlight, and make carbohydrates from water and carbon dioxide. During this process, they create oxygen as a waste product. – Once called blue-green algae, cyanobacteria are now known to be bacteria because they lack a membrane-bound nucleus and chloroplasts. Important Bacterial Groups, continued • Chlamydia – Gram-negative coccoid pathogens of the group Chlamydia live only inside animal cells. The cell walls of chlamydia do not have peptidoglycan. Chlamydia trachomatis causes the sexually transmitted infection called chlamydia. – Spirochetes are Gram-negative, spiral-shaped bacteria that move by means of a corkscrew-like rotation. Some are aerobic. – Spirochetes can live freely or as pathogens. Pathogenic spirochetes include Treponema pallidum, the causative agent of syphilis, and Borrelia burgdorferi, which causes Lyme disease. Structure and Function • The major structures of a prokaryotic cell include a cell wall, a cell membrane, cytoplasm, ribosomes, and sometimes a capsule, pili, endospores, and flagella. • Cell Wall – Most prokaryotes have a cell wall. Bacterial cell walls contain peptidoglycan. Archaeal cell walls do not have peptidoglycan; instead, some contain pseudomurein, a compound made of unusual lipids and amino acids. Structure and Function, continued • Structure and Function, continued DNA • Cell Membrane and Cytoplasm – Bacterial and archaeal cell membranes are lipid bilayers that have proteins. However, the lipids and proteins of archaeal cell walls differ from those of bacterial cell walls. – The cytoplasm is a semifluid solution that contains ribosomes, DNA, small organic and inorganic molecules, and ions. Structure and Function, continued • Capsules and Pili – Many bacteria have an outer covering of polysaccharides called a capsule that protects the cell against drying, pathogens, or harsh chemicals. – Pili are short, hairlike protein structures on the surface of some bacteria that help bacteria connect to each other and to surfaces, such as those of a host cell. • Structure and Function, Endospores continued – Prokaryotic DNA is a single closed loop of double-stranded DNA attached at one point to the cell membrane. – Along with a single main chromosome, some prokaryotes have plasmids, which are small, circular, self-replicating loops of doublestranded DNA. Bacterial Capsule Click below to watch the Visual Concept. Visual Concept Structure and Function, continued • Prokaryotic Movement – Some Gram-positive bacteria can form a thick-coated, resistant structure called an endospore when environmental conditions become harsh. – Many prokaryotes have long flagella that allow the prokaryotes to move toward food sources or away from danger. Structural Characteristics of a Bacterial Cell Parts of a Prokaryotic Cell Click below to watch the Visual Concept. Visual Concept Nutrition and Metabolism • Prokaryotes obtain nutrients either from the nonliving environment or by utilizing the products or bodies of living organisms. – Heterotrophs obtain carbon from other organisms. – Autotrophs obtain their carbon from CO2. – Chemotrophs get energy from chemicals in the environment. Bacteria and Health • Antibiotics and Antibiotic Resistance – A mutation in the DNA of a single bacterium can confer resistance to an antibiotic. – Cells with the mutant gene have a selective advantage when the antibiotic is present. – Mutant cells take over the population when the normal cells die. – This is a common example of evolution that is easily observed within a human lifetime Reproduction and Recombination • Genetic recombination in bacteria can occur by the following three ways: – transformation (taking in DNA from the outside environment) – conjugation (exchanging DNA with other bacteria via pili) – transduction (transmission of bacterial DNA via viruses). Bacteria and Health, • Emerging Infectious Diseases Caused by Bacteria – The number of certain bacterial diseases has increased because of the increase in the number of antibiotic resistant bacteria, the movement of people into previously untouched areas, and global travel. Bacteria in Industry • Many species of bacteria are used to produce and process different foods, to produce industrial chemicals, to mine for minerals, to produce insecticides, and to clean up chemical and oil spills. • Biologists have learned to harness bacteria to recycle compounds in a process called bioremediation, which uses bacteria to break down pollutants. Characteristics of Viruses • Viral Size and Structure – Viruses are nonliving particles containing DNA or RNA and are surrounded by a protein coat called a capsid. – Some viruses also have an envelope that is derived from a host cell’s nuclear membrane or cell membrane. Vectors of Viral Diseases • Vectors, or hosts, of viral diseases include humans, animals, and insects. Discovery of Viruses • Researchers in the late 1800s discovered that something smaller than bacteria could cause disease. • In 1935, Wendell Stanley demonstrated that viruses were not cells when he crystallized TMV, the virus that causes tobacco mosaic disease in tobacco and tomato plants. Characteristics of Viruses • Classification of Viruses – Viruses can be classified based on whether they have RNA or DNA, whether the RNA or DNA is single or double stranded and circular or linear, by capsid shape, and whether or not they have an envelope. Human Viral Diseases • Viruses cause many human diseases, including the common cold, flu, hepatitis, rabies, chickenpox, certain types of cancer, and AIDS. • Chickenpox and Shingles – Chickenpox and shingles are caused by the same varicella-zoster herpesvirus. Human Viral Diseases • Viral Hepatitis – Hepatitis, or inflammation of the liver, can be caused by at least five viruses. – Hepatitis A and hepatitis E can be spread by fecally contaminated food and water. – Hepatitis B, C, and D are spread by sexual contact, by contact with infected blood and serum, and by the use of contaminated needles. Human Viral Diseases • Acquired Immune Deficiency Syndrome (AIDS) – The human immunodeficiency virus (HIV) is an RNA virus spread by sexual contact, by contact with infected body fluids, and from mother to fetus. – HIV targets macrophages and thus damages the body’s immune system. The disease called acquired immune deficiency syndrome (AIDS) results. Human Viral Diseases • Viruses and Cancer – Some viruses contain oncogenes that can cause cancer, while other viruses convert proto-oncogenes, which usually control cell growth, to oncogenes. – The human papillomavirus (HPV) causes genital warts and 93% of all cervical cancers Emerging Viral Diseases • Emerging viruses usually infect animals isolated in nature but can jump to humans when contact occurs in the environment. – “Jump” means that the virus has mutated so that it can infect a human • The mutation usually occurs at least decades before the virus has an opportunity to infect humans • The mutation rate has been very important in the evolutionary history of viruses DONE !