Taxonomy Branch of biology concerned with the description, identification, nomenclature and classification of organisms Significance of Taxonomy Without

ut it, it will be very difficult to study organisms (no identity), to communicate findings Local names often differ greatly from place to place Scientific names of organisms are the same throughout the world and thus provides a standard and precise way of communicating about organisms Provides a comprehensive system of nomenclature and classification Essential to the progress of biology because it permits biologists to: o Gather together information on similar organisms o Clarify evolutionary relationships o Add to the information about a particular species without unnecessary repetition of previous work Description The assignment of features or attributes to a taxon o o Characters Features Character states Two or more forms of character A shortened description consisting of only those taxonomic characters which help in separating a taxon from other closely related taxa Forms the diagnosis o Characters are termed as diagnostic characters o Diagnostic characters for a taxon determine its circumscription

Taxonomists have agreed upon a method for classifying organisms that utilizes categories called ranks a) Artificial Classification Based on easily observable characters such as habit, color, number, form, or similar features Natural Classification Uses overall similarity in grouping taxa Phenetic Classification Makes use of overall similarity based on data from all available sources such as morphology, anatomy, embryology, phytochemistry, ultrastructure and all other fields of study Phylogenetic classification Based on evolutionary descent of a group of organisms

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Systematics Study of diversity of organisms Reflects phylogeny Evolutionary history of a group of organisms Phylogenetic tree A branching diagram that indicates common ancestors and lines of descent Primitive character o A trait that is present in a common ancestor and all members of a group Derived character o Present only in a specific lineage and is not present in a common ancestor Binomial System of Nomenclature (Linnaean System) 2 name system Introduced by Karl von Linne, a Swedish biologist in the mid-eighteenth century Scientific name consists of two Latinized words: Genus name + Specific epithet Ex. Oryza sativa L. Much easier than a 10+ word name under the old polynomial system Creates less confusion Binomial name = Scientific name Ranks or categories o Hierarchal classification includes from greatest to smallest 1) Domain <broadest> 2) Kingdom 3) Division 4) Class 5) Order 6) Family

Identification Also called determination The process of associating an unknown taxon with a known one Recognizing that the unknown is new to science and warrants formal description and naming Nomenclature The formal naming of taxa according to some standardized system Purpose: the determination of a correct name for a taxon For plants, algae and fungi, the rules and regulations for the naming of taxa are provided by the International Code of Botanical Nomenclature (ICBN) Classification The arrangement of taxa into some type of order Purpose: provide a system for cataloguing and expressing relationships between these taxa

7) 8) Example 1) 2) 3) 4) 5) 6) 7) 8) Note:

Genus Species <most specific> Domain: Eukaryota Kingdom: Plantae Division: Magnoliophyta Class: Liliopsida Order: Zingiberales Family: Musaceae Genus: Musa Species: Musa paradisiaca Members of the same family are more related than members of the same class

Shape: Cocci (sphere) Bacilli (rod) Helical (spiral) Structural Characteristics Cell wall: peptidoglycan (sugars and proteins) o Gram +: w/ peptidoglycan penicillin action o Gram -: little peptidoglycan, lipopolysaccharides; most pathogens; impede drug action Capsule: for adherence and protection Pili: for adherence and conjugation Motility

Species Biological Species Concept o A group of actually or potentially breeding natural groups that are reproductively isolated from other groups <Ernst Mayr, 1924> Taxonomic Approaches 1. Phenetic Approach Basis solely on phenotypic similarities and differences between organisms Cladistic Approach Basis of phylogenetic or evolutionary relationships Puts emphasis on inferences from fossil records, comparative anatomy, and embryology Numerical Taxonomy Makes extensive use of digital computers to determine the degree of similarity between organisms Molecular Taxonomy Most recent and emerging approach Makes use of molecular similarities to establish taxonomic relationships Cladistic analysis and molecular data have been pointing out problems in the 5-kingdom scheme

Flagella Helical Shape (spirochetes) Slime Taxis (movement away or towards a stimulus)

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Form and Function Nucleoid region (closed circular chromosome) Plasmids Asexual reproduction: binary fission Sexual reproduction (not meiosis): Transformation uptake of genes from the surrounding environment Conjugation direct gene transfer from 1 prokaryote to another Transduction gene transfer by viruses Endospore resistant cells for harsh conditions (250 million years) Nutrition and Metabolism a) Photoautotrophs o Photosynthetic o Harness light to drive the synthesis of organics (cyanobacteria) b) Chemoautotrophs o Oxidation of inorganics for energy o Get carbon from carbon dioxide c) Photoheterotrophs o Use light to generate ATP but get carbon in an organic form d) Chemoheterotrophs o Consume organic molecules for both energy and carbon saprobes (dead organic matter decomposers) o Parasites absorb nutrients from living hosts o Nitrogen fixation conversion of atmospheric nitrogen (N2) to ammonium (NH4) by Rhizobium e) Oxygen relationships: o Obligate aerobes o Facultative anaerobes o Obligate anaerobes

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The Three Domain System New data suggests two lineages in prokaryotes Results in 3 domains 1. Bacteria 2. Archaebacteria 3. Eukaryota

Prokaryotes and the Origins of Metabolic Diversity Kingdom: Monera (?) Domain: Bacteria Domain: Archaea

Prokaryotic Ecology Decomposers unlock organics from corpses and waste products Symbiosis between symbiont and host Mutualism (+, +) Parasitism (+, -) Commensalism (+, 0) Diseases: Opportunistic normal residents of host; cause illness when defenses are weakened Exotoxins bacterial proteins that can produce disease without prokaryote present (botulism) Endotoxins components of gram membranes (ex. Salmonella) The Origins of Eukaryotic Diversity The Endosymbionic Theory Mitochondria and chloroplasts were formerly from small prokaryotes living within larger cells

Plant Evolution Plants

Multicellular Eukaryotic Photosynthetic Autotrophs Adaptations for terrestrial colonization: 1) Vascular tissues 2) The seed 3) The flower

Protists Groups lacking mitochondria Early eukaryotic link Ex. Giardia (human intestinal parasite causing severe diarrhea);Trichomonas (human vaginal infection) 1. Euglenoids Autotrophic and heterotrophic flagellates Ex. Trypanosoma causes African Sleeping Sickness; transmitted by tsetse fly Alveolata Membrane-bound cavities (alveoli) under cell surfaces Dinoflagellates (phytoplankton) Ex. Plasmodium causes malaria Paramecium ciliates Algae Golden Browns Dinoflagellates Phytoplankton (diatoms) a) Rhodophyta Red algae No flagellated stages Phycobilin red pigment b) Chlorophyta Green algae Has chloroplasts Gave rise to land plants Ex. Volvox, Ulva Mycetozoa Slime molds Not true fungi Use pseudopodia for locomotion and feeding Plasmodial and cellular slime molds

Plant Origins Charophytes o Green algae o Closest plant ancestor Similarities a) Homologous chloroplasts chlorophylls a and b b) Biochemical similarity cellulose composition; peroxisomes c) Cell division similarity mitosis; cytokinesis d) Sperm similarity in ultrastructure e) Genetic relationship nuclear genes; rRNA Characteristics That Separate Plants from Algae Ancestors Apical meristems localized regions of cell division Multicellular, dependent embryos embryophytes Alternation of generations gametophyte and sporophyte Walled spores produced in the sporangia Multicellular Other Terrestrial Plant Adaptations 1) Cuticle 2) Stomata 3) Xylem and phloem 4) Secondary compounds 1. Bryophytes o Mosses, liverworts, hornworts st o 1 to exhibit the embryonic condition: o Male = antheridium o Female = archegonium o Flagellated water sperm o No vascular tissue imbibe water o No lignin short stature o Dominant generation: haploid gametophyte Pteridophytes o Seedless vascular plants o Ferns, club moss, horsetails o Has true roots and leaves o Roots have lignified vascular tissue o Dominant life cycle: sporophyte o Homosporous plants a single type of spore o Sporophyte single type of spore o Bisexual gametophyte

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Eggs; sperm flagellated, damp locations Carboniferous period plants Plant Diversity II: The Evolution of Seed Plants Fungi Diversity 1. Chytridiomycota Aquatic fungi/chytrids Lineage closest to protists (flagella) 2. Zygomycota Rhizopus (food mold) Mycorrhizzae mutualistic with plant roots Zygosporangia 0 resulent structure (freezing and drying) Ascomycota Sac fungi yeasts, truffles, morels, sordaria Asci sexual spores Conidia asexual spores Basidiomycota Club fungus mushrooms, puffballs, shelf fungus, rust Basidiocarps produce sexual spores

Seed Plant Reproductive Adaptations 1. Reduction of the gametophyte 2. Advent of the seed 3. Evolution of pollen Seed Plants 1. Gymnosperms Gingko, cycads, conifers Cone-bearing plants Lack enclosed chambers (ovaries) for seeds Ovules and seeds develop on specialized seeds called sporophylls All are evergreens Needle-shaped leaves Vascular tissue refinement- tracheids, which are water conducting and supporting elements of the xylem Angiosperms Most diverse and geographically widespread of all plants flowering plants 1) Monocots 1 embryonic seed leaf Ex. Lilies, palms, grasses, grain crops 2) Dicots 2 embryonic seed leaves Ex. Roses, peas, sunflowers, oaks, maples

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Specialized Lifestyles 1. Molds Only the asexual stage present (asexual spores) Penicillin (antibiotic, cheese) Yeasts Unicellular Asexual budding Saccharomyces (bread, alcohol) Lichens Symbiotic association held in a hyphae mesh Algae provides the food, fungus provides physical environment Pioneer organisms Function in air pollution detection Mycorrhizae Root and fungi mutualism

Fungi Diversity Fungi

Heterotrophic by absorption (exoenzymes) Decomposers (sabrobes) Parasites Mutualistic Symbionts (ex. Lichens)

Fungi Body 1. Hyphae Body filaments a) Septate with cross walls b) Coenocytic without cross walls 2. 3. Mycelium Network of hyphae Chitin cell walls Polysaccharide with nitrogenous group