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Diversity of Microbes I. Diversity of Life A. Gaia Hypothesis i.

Earth is a living entity and its biosphere regulates and maintains climate and atmosphere at an optimum B. Aquatic Ecosystems i. 97.5% is salt water & 2.5% is fresh ii. 71% of Earth surface occupied by ocean iii. Mean depth of ocean 3.8 km as deep as 11 km iv. Total volume is 1.4 x 107 km3 v. 300 X more space for life than on land or fresh water vi. Inhabited by at least microbes C. Human Body i. A microbial system 90% non-human ii. 10X more bacterial cell than human 1. Help to digest food 2. Help to fight pathogens 3. Help provide vitamins D. Aquatic Microbes i. Bacteria ii. Archaea iii. Protists iv. Fungi v. Viruses E. Where did water come from? i. Degassing and condensation ii. Comet impact bring ice to earth iii. Asteroid impact H2O inside asteroids brought to earth iv. Ratio of heavy : normal H20 providing clues F. *Microfossils ~ 3.5-3.8 billion years old G. What constitutes life? (Essential characteristics) i. Membranes ii. Aqueous system iii. Monomers to macromolecules iv. Information carriers (RNA/DNA) and translation apparatus

v. Energy storage & flow vi. Catalysts H. How did life originally evolve? i. Vital force view: Life is different than forces found in physics/chemistry (Not testable via science) ii. Mechanistic view: Life is chemically based and composed of the same elements as the inanimate universe with a UNIQUE and PARTICULAR assignment I. Spontaneous Generation i. Do some forms of life arise repeatedly and directly from inanimate matter? ii. 1665: Francesco Redi Life generates life iii. 1884: Louis Pasteur Airborne microbes J. Origin of Life on Earth i. Hypothesis I: Extraterrestrial OriginPanspermia 1. Theory that life exists and is distributed throughout the universe in the form of germs or spores 2. Life may not be unique to earth ii. Hypothesis II: Chemical Evolution 1. Origin of life can be viewed as four overlapping stages a. Stage 1: Nucleotides and amino acids before cells i. Extraterrestrial input hypothesis: organic matter and water brought to earth via asteroid and comet collisions with earth ii. Reducing atmosphere hypothesis (Chemical evolution) 1. Volcanic out gassing strongly reducing atmosphere (H20, Cl, H2, CH4, H2S, NH3, CO2) 2. There was little or no O2

3. Miller-Urey Experiment: Could key organic molecules have formed in the conditions of early Earth? a. Simulated biological conditions without oxygen b. Produced nucleotides and amino acids, precursors for DNA and proteins/enzymes iii. Hydrothermal Vent Hypothesis: Temperature gradients and plume chemistry formation of organic molecules b. Stage 2: Nucleotides and amino acids polymerize i. DNA, RNA & proteins ii. How did macromolecules form from monomers without the aid of enzymes? iii. Concentration of monomers at edges at hot pools polymerization iv. Metal (nickel and iron) polymerization of amino acids without O2. c. Stage 3: Polymers enclosed in membranes i. Protobionts Aggregate of abiotically produced organic molecules that can have metabolism ii. Coacervates cant reproduce but have internal chemistry different from surrounding environment 1. Mixture of protein and polysaccharides form coacervates d. Stage 4: Evolution of cellular properties i. How do you get from non-living chemical blob like a protobiont to a living cell? ii. Need: 1. Catalyst 2. Information carrier and transfer 3. Energy

iii. Catalytic RNA RNA folding (H bonds stabilize in 3-D form) iv. Ribozymes Thomas Cech (1980) v. RNA world: 1. Acted as both information carrier 2. Catalyst II. The History of Life on Earth A. Dating i. Fossils 1. Stratigraphic Relationship a. Can determine relative ages of fossils b. Similar types of fossils found within strata in widely separated parts of the earth c. Major changes in fossil types in the rock strata used to define time periods 2. Absolute dating using radioactive decay a. Radioactive isotopes decay over regular equal periods of time b. If you know how much isotope existed at the beginning and you know how much remains you can calculate the age of the sample c. Ratio of radioisotope to stable isotope provides info about how many half-lives have passed ii. Geologic and Biogeochemical changes that affected extinction and evolution 1. Continential Drift sea level fall 2. Climate change 3. Volcanic activity 4. Unidirectional in O2 5. External events III. Phylogeny & Introduction to Microbiology A. Changes in living organisms are a result of two interactive processes: i. Genetic exchange affects their characteristics allows them to survive in given environment

ii. Environmental change influences type of organisms that have existed during different periods B. Taxonomy and Systematics i. Taxonomy 1. Theory and practice of classifying organisms ii. Phylogeny 1. Classifying organism based on evolutionary history iii. Systematics 1. The science of studying diversity of organisms and reconstructing phylogeny C. Molecular Phylogeny i. rRNA 1. Structural gene evolutionarily ancient 2. Highly conserved all living organisms have it, plays same role in translation in all organisms 3. Yet sufficient variability to denote difference between organisms ii. Pairwise Evolutionary Distance 1. Squence rRNA gene 2. Align homologous sequences 3. Count differences 4. Calculate pairwise evolutionary distance 5. Phylogenetic tree iii. Microbes occupy all three of the main domains of life 1. Based on 16s or 18s rRNA gene sequences Carl Woese 2. All prokaryotes are microbes and some eukaryotes are microbes 3. 2 entire domains are microbes (Bacteria + Archaea) 4. A full 1/3 of the other are microbes (Eukaryota)


Microbes and Brief History of Microbiology A. Microbes i. Single cell or cell cluster ii. Stand-alone organisms iii. Capable of living independent of tissue 1. Growth 2. Energy generation 3. Reproduction B. Traits that set microorganisms apart from non-living chemical systems: i. Metabolism 1. Uptake of chemicals from environment, their transformation within cell, and elimination of wastes into environment (open system) ii. Reproduction (growth) 1. Chemicals from environment are turned into new cells under direction of preexisting cells iii. Differentiation 1. Formation of a new cell structure such as a spore, usually a part of a new cellular life cycle iv. Communication 1. Cells communicate or interact primarily by means of chemicals that are released or taken up. v. Movement 1. Living organisms are often capable of self-propulsion vi. Evolution 1. Cells evolve to display new biological properties 2. Phylogenetic trees show evolutionary relationships between these cells C. Common Features Between Microbes i. Live in water ii. Food for higher trophic levels iii. All are small Higher surface area to volume ratio

1. Increased efficiency for nutrient uptake and waste removal 2. Higher proportion of metabolically active body components 3. Higher growth rates 4. Example: Phytoplankton make up only 0.2% of all living plant matter on earth, yet account for 45% of the earths photosynthetic activity D. Importance of Microbes i. Most abundant organisms in the biosphere contain enormous amounts of biomass ii. Vast physiological diversity 1. Macrobes have only 2 distinct physiologies a. Photosynthesis (chloroplasts) b. Heterotroph (mitochondria) 2. Microbes (specifically prokaryotes) have hundreds a. Ammonia oxidizers NH3 NO2 b. Iron oxidizers Fe2+ Fe3+ c. Sulfate reducers SO4 H2S d. Sulfur oxidizers H2S SO4 iii. Basic Metabolic Strategies 1. Photosynthesis (Photoautotrophy) a. Phytoplankton b. CO2 + Nutrients Organic Matter + O2 2. Respiration (Heterotrophy) a. Bacterioplankton b. Organic Matter + O2 CO2 + Nutrients 3. Sulfur Oxidizing Bacteria a. Base of food web at the hydrothermal vents b. H2S + 2O2 SO4 + 2H+ iv. Major Biogeochemical Agents 1. Chemical difference between Earths crust and living organisms 2. Macro nutrients (C,H,O,N,P,S) 3. Cells are nonequilibrium systems v. Control Human History 1. Human evolution sickle cell malaria

2. Population dynamics Bubonic plague 3. Migration potato blight vi. Industry 1. Agriculture N2 fixation, nutrient cycling 2. Biotechnology pharmaceutical production, gene therapy 3. Energy/ environment biofuels, bioremediation 4. Food preservatives, alcohol, cheese, pickles E. History of Microbiology i. Many advances in microbiology have come from technological developments particularly those that extend our senses 1. 1684 Van Leeuwenhoek used crude microscope to observe bacteria and protists ii. Most early work focused on issues directly related to humans iii. Young science iv. Microscopy 1. Magnification 2. Resolution Distance apart 2 objects to distinguish them as separate 3. Magnify no more info 4. Increase resolution gain info v. Louis Pasteur 1. Industrial Microbiology a. Disproved theory of spontaneous generation 2. Pasteurization a. Got microbes into culture b. Worked on theory and practice of vaccination c. Proved that microbes were responsible for biodegradation d. Different microbes produce different products vi. Robert Koch 1. Medical Microbiology a. Develoed pure culture technique b. Assumed colonies with different shapes and colors were derived from different microbes c. Isolated one colony and restreaked plate

2. Suspected pathogen should be present in all diseased and absent from all healthy organisms 3. Suspect pathogen should be grown in pure culture 4. Cells from pure culture should cause disease in healthy organism 5. Pathogen should be reisolated and shown to be the same as original vii. Sergei Winogradsky 1. Environmental Microbiologist a. Developed first ideas of chemolithotrophy 2. Chemolithotrophy organisms obtain their energy from the oxidation of inorganic compounds and use CO2 as carbon source (autotrophs) viii. Martinus Beijerinck 1. Environmental Microbiologist a. Discovered enrichment cultures 2. Set up culture with all inorganic nuts except N if bugs were going to grow, they would have to fix it


Brief History & Prokaryotic Diversity A. Molecular Biology studying microbes through their genes B. Used molecular sequence of rRNA genes to reconstruct phylogenetic relationship C. Thermus aquaticus i. Discovered by Environmental microbiologist - Thomas Brock and Hudson Freeze ii. Isolation of microbes from hot spring source of thermally stable polymeraseuse in PCR

D. Norman Pace i. Developed Cultivation independent techniques ii. 16s rRNA gene clone library construction iii. Sample of culture or environmental biomass iv. Lyse cells, extract DNA, and amplify 16s rDNA (PCR) v. Insert ligate 16s rDNA strands into plasmids vi. Transform (introduce) plasmids into E.coli cells vii. Pour transformed culture onto plate viii. Pick white colonies, grow in media (one colony per tube) ix. Archive clones and sequence x. RESULT: E. coli cells containing 16s rDNA from one member of original culture E. Identifying an Organism via rRNA Genes i. Isolate plasmids from clone ii. Sequence rRNA gene ligated in plasmids iii. Align sequence data to assess variability iv. Construct phylogenetic relationship F. Genomics Era i. Craig Venter 1. Used a random shotgun sequencing approach a. Step 1: Library construction i. Break genomic DNA from organism into many small fragments ii. Fragments are cloned into plasmid vectors iii. Transform into E. Coli iv. Collection of fragments is called a library b. Step 2: DNA Sequencing i. The fragments are sequenced using a process called chain termination DNA sequencing c. Step 3: Assemble Fragments i. Sequencer output assemble fragments closure & annotation 2. Human Genome project 3. 500 microbial genomes 4. Sargasso Sea metagenome

5. Global Ocean survey ii. Genome: the entire genetic make-up of an organism iii. Metagenome: study of genomic material from a mixed population G. Microbial Gene List i. Genes can be found within a sequence by computer modeling programs ii. These can be compared to known genes to determine a function of the gene iii. Vibrio cholera (Metabolism) iv. Open reading frame (ORFs) portion of genetic code the codes for proteins v. Way to make aritifical life Have software make hardware JC Venter 1. Synthetic genome 2. Objective to create a microbe that converts CO2 to fuel VI. Prokaryotic Diversity A. Quick Review i. Prokaryotes 1. Cell walls 2. No organelles (no microtubules) 3. Nucleoid and free ribosomes ii. Eukaryotes 1. Organelles 2. Cytoskeleton (microtubules) 3. Can digest material internally B. Nuclear Material i. Prokaryotes 1. Circular DNA 2. 1 chromosome 3. No membrane separating transcription and translation 4. 1/1000 as much DNA as Eukaryote 5. Ribosomes are slightly smaller ii. Eukaryotes 1. More genesmore DNA 2. Several linear pieces of DNA

3. Nucleus contains DNA separation, transcription and translation 4. DNA contains large amount of repeating sequence and introns C. DNA Transfer i. Prokaryotes 1. Asexual reproduction 2. Cloning ii. Eukaryotes 1. Sexual reproduction 2. Chromosome transfer D. Lateral gene DNA transfer: the gene of one species is incorporated into another 1. Three mechanisms for prokaryotic genetic recombination a. Transformation b. Conjugation c. Transduction 2. How do we differentiate between different prokaryotes? a. Morphology 3 main shapes i. Cocci (sphere) ii. Bacilli (rod) iii. Spirochetes (spiral) b. Biochemical characteristics i. Cell wall, cell membrane structure ii. Metabolic strategy iii. Relationship to O2 iv. Relationship to temperature E. Cell Membranes i. Bacteria phospholipid bilayer 1. Gram stain used to separate to bacteria into 2 groups: a. Gram +: simpler cell wall i. Less physiologically diverse ii. Can produce exotoxins b. Gram -: more complex, lipopolysaccharides (LPS) attached (can produce endotoxins)

c. Bacteria have peptidoglycan cell wall whereas Archaea do not have peptidoglycan ii. Archaea phospholipid bilayer (no fatty acids) 1. Isoprene instead 2. Some have monolayer vs bilayer F. Nutritional Requirements for Anabolism i. Energy Source 1. Chemotrophy vs Phototrophy ii. Carbon Source 1. CO2 Autotroph 2. Organic C - Heterotroph

G. Energy Generation i. All organisms on this planet generate their ATP using one of three processes: 1. Fermentation substrate level phosphorylation no external electron acceptor 2. Oxidative or Electron Transport Level Phosphorylation (ETLP) a. Anaerobic use NO3-, Fe3+, SO42-, and CO32- as electron acceptor b. Aerobic uses O2 as electron acceptor i. Uses electron transport system and proton motive force

3. Phosphorylation a. Light energy generates proton gradient and proton motive force i. Proton motive force: electron carriers are oriented in membrane that separates protons from electrons H. Prokaryotic General Biology i. Phototrophs 1. Bacteriorhodopsin a. Synthesis of ATP without chlorophyll pigment 2. Primitive photophosphorylation a. Absorbs light and pimps H+ ions out b. Protein gradient then used to generate ATP 3. Purple & Green Bacteria a. Anaerobic b. Photosystem I anoxygenic 4. Cyanobacteria a. Obligate photoautotrophs b. Photosystem II c. Light for energy source d. Oxygenic process (source of O2 on Earth) ii. Photoautotrophs 1. Some use CO2 for C source and light energy is used to split H2S and H2 instead of water purple sulfur iii. Photoheterotrophs 1. Many use light for energy and organic C for C source purple non sulfur iv. Chemoautotrophs 1. Sulfur oxidizers 2. Hydrothermal vent communities first degree production base of ecosystem v. Microbial Mining: Method of extracting sulfide ore 1. Cu2S Cu2+ + SO4 2. Thiobacillus gains energy from oxidizing both Cu and S

vi. Chemoheterotrophs: majority of prokaryotes 1. Saprobes feed on dead organic matter 2. Parasites vii. Pseudomonads 1. Generic gram - heterotroph 2. Aerobic 3. Fast growing 4. Use simple compounds viii. *Resulting biogeochemical responses from oxygenic photosynthesis 1. O2 attacks bonds of organic matter 2. Organisms developed antioxidant mechanisms 3. Production of ozone shield UV interacts with O2 O3 VII. Prokaryotic Diversity and Protists A. Metabolic Relationship to Oxygen i. Obligate Aerobe (require O2) 1. Organic C CO2 + H2O ii. Microaerophiles 1. Use O2 for respiration but cant handle full atm. iii. Facultative Anaerobe 1. Switch physiologies 2. w/ O2 Respiration 3. w/o O2 Fermentation iv. Obligate Anaerobe (O2 is toxic) 1. SO4 H2S B. Temperature prokaryotic range < 0 to 110 C i. Psychophiles low temps -- < 0 20 ii. Mesophiles midrange temp 20-48 iii. Thermophiles high temp 4268 iv. Hyperthermophile very high temp 65-110

C. Phylogeny & Diversity i. Classification of Bacteria and Archaea Based on molecular systematics ii. Bacteria 1. Proteobacteria a. Largest and most diverse group 2. Purple Bacteria a. Photoautotrophic & photoheterotrophic 3. Rhizobium a. Nitrogen fixing symbiont 4. Enteric Bacteria a. Inhabit intestinal tract, facultative anaerobes b. i.e. E. coli, Salmonella, Y. pestis 5. Cyanobacteria a. Obligate photoautotroph b. Photosystem II c. Some form colonies 6. Low GC Bacteria a. Firmicutes endospores (Clostridium botulinum) 7. High GC Bacteria a. Actinomycetes (filaments) i. Mycoplasmas (no cell wall) 8. Spirochetes 9. Chlamydias D. Prokaryotes to Eukaryotes (Big Changes) i. Loss of cell wall flexibility increases --- infolding surface area increases 1. 1st step to organized nucleus ii. Ribosome studded internal membrane iii. Appearance of cytoskeleton gave physical structure to big cells iv. Formation of digestive vesicles v. Endosymbiosis of organelles E. Characteristics of Protists i. Most are aquatic ii. Nutritional Diversity

1. Protozoa animal like 2. Algae plant like 3. Fungus like iii. Locomotion 1. Pseudopod 2. Cilia 3. Flagella iv. Organelles and Vesicles 1. Cells can be large surface/area ratio can be a problem 2. Endocytosis: process of taking in food within vacuoles formed by invagination of the plasma membrane 3. If dissolved, called pinocytosis 4. If particle, called phagocytosis 5. Contactile Vacuole assist in osmoregulation v. Cell Surfaces: Diverse vi. Endosymbionts 1. Foraminifera vs. Radiolarians vs. Acantharia vii. Reproduction Processes 1. Asexual a. Binary fission b. Multiple fission c. Budding d. Spores 2. Conjugation Genetic recombination in paramecia a. Sexual but not reproductive process b. Ciliates have two types of nuclei 3. Sexual Reproduction: Many protists life cycles have alternation of generations a. Heteromorphic Haploid and diploid generations are morphologically different b. Isomorphic Haploid and diploid generations are morphologically the same F. Examples of Protists i. Diplomonads and Parabasalids 1. All lack mitochondria

2. Obligate parasites ii. Euglenids 1. No cell wall 2. Heterotrophic & photoautotrophic iii. Dinoflagellates 1. 2 flagella of different sizes 2. Bioluminescent 3. Red tides 4. Endosymbionts 5. Auto, mixo and heterotrophs iv. Cilliates VIII. Microbial Eukaryotes Continued.. A. Alveolates: Dinoflagellates i. Alveolata (contain alveoli sacs below plasma membrane support?) ii. 2 flagella of different sizes and positions iii. Phytoplankton iv. Red tides v. Apicomplexans 1. Parasites of animals, with unusual spores 2. Apical complex is defining structure used to burrow into host tissue or cells 3. Intricate life cycle (i.e. Plasmodium parasite malaria) vi. Coccolithophorids 1. CaCO3 plates, coccoliths 2. Autotraphic 3. Ocean acidification will have major effect 4. Huge blooms visible from satellites B. Stramenopila: Diatoms i. Carotenoids, yellow/brown in color ii. Silica shells iii. Important marine phytoplankton (20% of Earths photosynthetic production more than 50% of the oceans production) iv. Asexual and sexual reproduction v. Harmful algal blooms (Pseudonitzschia)

vi. Diatomaceous Earth vii. Brown Algae 1. Phaeophyceae 2. Photoautotrophs 3. Fucoxanthin pigment 4. Multicellular (seaweeds) 5. Macrocystis Giant Kelp is brown algae C. Plantae i. Ancestral trait: Primary endosymbiosis with a cyanobacteria ii. Include most unicellular and colonial algae iii. Most likely precursor to all plants iv. Chlorophytes (green algae) 1. Pigments are Chlorophyll a and Chlorophyll b 2. Examples include many species (17,000 worldwide) and many life forms (unicellular, multicellular, colonial) D. Rhodophyta (red algae) 1. Have no flagellated stages 2. Key pigment: phycoerythrin 3. All are multicellular (no free-living unicellular) 4. Some secret CaCO3 5. Coralline algae are important for reef building E. Excavates i. Mostly heterotrophs ii. Kinetoplastids 1. Trypanosoma-african sleeping sickness iii. Diplomonads 1. Giardia lost mitochondria iv. Euglenids are often Mixotrophic F. Rhizaria i. Primarily marine, some freshwater ii. Many have photosynthetic endosymbionts, but most are heterotrophic iii. Amoeboids with complex shell-skeletons 1. Radiolaria have silica skeletons 2. Foraminifera have CaCO3 skeletons

a. Highly susceptible to ocean acidification G. Unikont: Amoebozoa i. Pseudopodial extension of cytoplasm ii. Heterotrophic phagocytosis 1. No cell walls iii. i.e. Slime molds (2 groups) 1. Plasmodial slime molds 2. Cellular slime molds H. Unikont: Choanoflagellida i. Closest relative to animals ii. Colonial iii. Similar to sponges IX. Characteristics of Fungi A. Heterotrophic eukaryotes (molds, yeast, mushrooms) B. Chitin in cell walls C. Chemoorganotrophs w/ absorptive metabolism D. Produce spores (almost all) E. Saprobic, parasitic, mutualistic fungi F. Tolerance to hypertonic environments G. Tolerant to low -6C and high (50C) temperatures H. Good at degrading complex polymers (cellulose, lignin, humic) I. Produce secondary chemical byproducts: i. Antibiotics: penicillin, cephalosporin ii. Alkaloids ergot, lysergic acid (LSD) iii. Toxins aflatoxins, psilocybin J. Unicellular Fungi i. Unicellular members of all fungal groups ii. Collectively called Yeasts in higher fungi iii. Many fungi can alternate between unicellular and multicellular forms via alternation of generations K. Multicellularity in Fungi i. Mycelium: The body of a multicellular fungus ii. Mycorrhizae: Associations between vascular plant roots and fungal mycelia

L. Hyphae i. Septate incomplete cross walls ii. Coenocytic no septa iii. Haustoria push into cells parasite M. Reproduction and Sporulation i. Dikaryotic life stage in higher crown fungi ii. Fruiting bodies are called sporangia iii. Air: 10,000 fungal spores per cubic meter 1. Each breath = 5 spores iv. No motile gamete stage (terrestrial) v. Fungi reproduce both sexually and asexually vi. Mating types rather than male and female vii. Dikaryon (n+n) not diploid viii. Asexual favorable conditions ix. Sexual unfavorable conditions N. Ecology of Fungi i. Lakes and ocean limited role ii. Streams more important 1. Lead litter more surfaces iii. Terrestrial prime remineralizer 1. Filamentous growth: spread through soil 2. Translocate resources O. Symbiotic Mutual Relationships i. Lichens: 1. Symbiotic complex of fungi & algae or cyanobacteria 2. Pioneer organisms 3. Fungi get C sometimes N from algae or cyanobacteria 4. Algae get nutrients, water & protection from: a. High light b. Dessication c. Grazing P. Main Groups of Fungi i. 100,000 species identified ii. Key fungal groups defined primarily by reproductive forms and lifestyles

iii. Glomeromycota: Arbuscular Mycorrhizae 1. Mutualistic infection 2. Vascular plant: a. Prevent desiccation b. Helps with uptake of nutrients c. Increase absorbing area d. Protection against attack 3. Fungi: a. Receives organic substrates 4. Chytrids a. No dikaryotic stage b. Aquatic c. Flagellated 5. Zygomycota a. Coenocentric hyphae b. Rapid spreading growth (think mold) c. Zygosporangia (no big fruiting body) 6. Ascomycota a. Sac fungi (sex spores made in asci) b. Septate hyphae c. Large fruiting bodies Ascocarps d. Include many plant pathogens: i. Penicillum mold (source of Penicillin) ii. Ergot of rye hallucinogenic 7. Basidiomycota a. Mushrooms Q. Viruses i. Not cells 1. Nucleic acid + protein only 2. No transport regulation via membranes 3. No metabolic functions ii. Can reproduce 1. Obligate intracellular parasites 2. Use host replication machinery

iii. Host Specificity: Not all hosts are created equal iv. Host Range 1. Can parasitize a limited range of hosts 2. Need appropriate receptor sites 3. Contact host by passive diffusion and use host exposed cell surface as attachment sites 4. Encounter rate is proportional to density of host v. Viruses hijack the host cell to replicate their genes 1. Attachment 2. Injection 3. Virus enzymes synthesized 4. Nucleic acid replication 5. Synthesis of protein coats 6. Assembly & packaging 7. Release vi. Transduction results when bits of host DNA are packaged in viral capsules 1. Concept useful for targeted gene therapy a. Keep replication machinery, replace disease genes

Diversity of Plants I. Plants A. Uses i. Food & feed ii. Spices and herbs iii. Beverages iv. Shelter v. Drugs vi. Paper & Rope vii. Clothing viii. Rubber B. History i. Origin of Agriculture Shaping human culture ii. Virtually all civilizations based on domestication of a cereal crop (a monocot) 1. Maize Americas 2. Rice Asia 3. Wheat Middle East iii. Much of the exploration of the world during 15th and 16th centuries was in search of spices C. What are Plants? i. *A plant is a photosynthetic eukaryote that uses chlorophylls a and

b, stores starch, and develops from an embryo protected by tissues

of the parent plant 1. Because of their development from embryos, plants sometimes referred to as embryophytes 2. Kingdom Plantae is monophyletic, forming a single branch of the evolutionary tree ii. Multicellular iii. Photosynthetic (mostly) iv. Eukaryote v. Cell walls cellulose vi. Storage starch vii. Terrestrial (mostly) viii. Embryos protected by tissue of the parent plant (EMBRYOPHYTES)

D. Classification of Plants i. Many ways to classify ideally, try to identify monophyletic groups 1. Have synapomorphies (shared derived characters) that define the group ii. Charophytes most closely related group to Land plants 1. Homologous chloroplasts a. Chlorophyll a & b b. Beta-carotene as accessory pigments c. Thylakoid membranes stacked as grana d. Store starch 2. Biochemically similar a. Cellulose major component of cell walls 3. Similarity in mitosis & cytokinesis a. Use of cell plate rather than cytoplasmic constriction or cell furrowing 4. Genetic Relationship a. cpDNA similar, rDNA & other nuclear genes 5. Which living charophyte algae is the closest relative to the embryophytes? a. Terrestrial vs. Aquatic? b. Unicellular filamentous or flattened (leaf like)? E. Move to Land Biggest ecological shift i. Cuticle Needed for retention of water ii. Stomata Needed for gas exchange and retention of water iii. Division into subterranean & aerial organs Needed to transport between medium

iv. Lignin Needed for support in arial environment (woody portions of plants) v. Gametangia Protection of gametes from dessication vi. Sporopollenin & thick spore walls Needed for protection from dessication and resistant to damage vii. Mutualistic association with a fungus viii. Embryos Young sporophytes protected F. Types of Life cycles i. Haplontic 1. E.g. Rhizopus ii. Alternation of generations 1. Which generation dominates the life cycle helps to classify plants 2. E.g. Embryophytes iii. Diplontic 1. E.g. Snake G. Non-Tracheophytes i. Descendents of the oldest lineages of plants (Non-vascular) ii. Widely distributed iii. Usually very moist habitats iv. Gametophyte dominates v. Examples: 1. Liverworts a. No filamentous stage b. Gametophyte flat 2. Hornworts a. Embedded archegonia b. Sporophyte grows basally 3. Mosses a. Filamentous stage b. Sporophyte grows apically (from the tip)


Tracheids A. Specialized cells B. Spindle shaped C. Interconnected by pits D. Provide structural support E. Formed through programmed cell death F. Function for transport of water and nutrients after they die G. The first tracheophytes i. Lacked true leaves ii. Lacked roots iii. Had xylem (i.e. tracheids) iv. Tetrahedral sets of cells indicate that they are products of meiosis H. Ferns & Fern Allies i. Have features not found in any earlier groups 1. True roots a. Dichotomous branching may have allowed the evolution of specialized root and shoot axes 2. True leaves a. A leaf is a flattened photosynthetic structure emerging laterally from a main axis or stem and possessing true vascular tissue b. Simple leaves characteristic of the Lycophytes (Club Mosses) c. Complex leaves have multiple vascular strands and may have evolved independently in several different groups 3. Heterospory a. Promotes outcrossing b. Provides flexibility for development c. Endosporic development of the megagametophyte

I. Lycophyta (Club Mosses or Ground Pines) i. 1000 spp in 10-15 genera ii. Fossils as early as Devonian iii. Mostly small now but during Carboniferous Trees iv. Presently grown in NE US and Canada v. Most species are in trophic (epiphytes) vi. Sporangia arranged in strobili rather than simply terminal as in Rhynia vii. Dichotomous branching (shoots & roots) viii. Simple leaves ix. Some heterosporous J. Monilophytes (Ferns) i. 12,000 spp ii. Most diverse in the Tropics (3/4 of all species) iii. Coal Age Plants see fossils iv. Large diversity 1. Climbing & twining 2. Tree ferns 3. Water ferns v. Examples: 1. Azolla 2. Salvinia 3. Marsilea (floating aquatic fern) 4. Pteris vittata (brake fern) a. Accumulates arsenic b. Can be used in Phytoremediation c. Cleaning up toxic waste sites using plants 5. Wisk ferns (2 genera) a. Once suggested that they were the direct descendents of the Rhyiophytes

b. Now know that the morphology is recently derived and that their closest relatives are all ferns 6. Horsetails or Scouring Rush a. Fossils as early as Devonian b. Carboniferous giant Trees c. Moist or damp places d. Worldwide (except Australia & New Zealand) e. Used to scour pots & pans in Colonial & Frontier times III. The Seed Plants A. Gametophyte is reduced even further than in non-seed tracheophytes B. No need for external water for sexual reproduction C. Haploid megagametophyte develops partially or entirely while attached to and is nutritionally dependent on the diploid sporophyte D. Male gametophyte is a gene dispersal stage (i.e. pollen) E. Seeds, which contain the new sporophyte generation, are a resting (i.e. dormant) stage and are a means of dispersal F. Gymnosperms (Naked seed) i. Ovules and seeds not protected by flower and fruit, respectively ii. Strobilus = cluster of modified leaves with sporangia iii. Microsporangium microgametophyte iv. Generative cell (1n) undergoes mitosis to produce two sperm cells v. Pollen grain (1n) = multicellular vi. Young female cone (ovules containing megasporangium) vii. Mature female cone (seeds) G. Pollen i. Microgametophyte ii. Dispersal stage (unlike the non-tracheophytes and the non-seed tracheophytes) iii. Innovation for the avoidance of inbreeding

H. Ovule i. Structure containing female gametophyte (and egg cell) surrounded by the nucellus (megasporangium) and one or two integuments ii. Seed = Mature ovule 1. Provides a protective environment for the developing embryo (sporophyte) 2. Seed in resting stage = can stay dormant for long periods of time and then grow under favorable conditions 3. Seeds provide a nutrient reserve for the germination and growth of the embryo 4. Seeds often have adaptations for dispersal iii. Fertilization of egg may not occur until after the ovules have been shed iv. Some seeds are considered as a delicacy and used as herbal medicine v. Trees largely resistant to smog and are planted in many cities IV. Angiosperms A. Flowers B. Double fertilization C. Triploid endosperm D. Ovules enclosed in carpel E. Seeds enclosed in fruit F. Xylem vessels & fibers G. Phloem companion cells H. Tracheids may have evolved into two new types of cells: i. Vessel elements water transport ii. Fiber cell support

I. Evolution of the Flower i. Fusion of carpels into one pistil 1. Efficient deposition of pollen and movement of pollen tubes down one or few style lobes ii. Exotic landing platforms, spurs, nectaries, etc. 1. Specialization for specific pollinators iii. Closed carpel 1. Protection of ovules and seeds 2. i.e. Drimys basal angiosperm iv. 97% of Angiosperms are either Monocots or Eudicots 1. Monocots a. Single cotyledon in seeds b. Narrow leaves c. Parallel veins d. Flower parts in 3s e. Vascular bundles scattered in the stem 2. Eudicots a. Two cotyledons b. Broad-leaves c. Net-like veins d. Flower parts in 4s or 5s e. Vascular bundles in a ring in the stem v. Diversity of Pollination Mechanisms 1. Wind dispersal 2. Simple fruit, from a single carpel 3. Animal dispersal, active a. Ant dispersal b. Bat fruit dispersal c. Fly pollination i. Fly flowers (strong, fetid odor; dull color; small clusters) d. Bee & Wasp Pollination i. Flowers are white, blue, yellow generally not red ii. Strong UV light patterns

iii. nectar guides iv. Fig Wasp pollination 1. Host specificity by female wasps who lay eggs in gall forming fig ovaries but pollinate other ovaries e. Moth Pollination i. Darwin predicted a hawkmoth would be found with foot-long proboscis for the Malagasy Christmas Star ii. Xanthopan morgana praedicta was discovered on the island with a 12 inch tongue forty years later iii. Flowers usually white, long tubes, night blooming iv. *Butterfly flowers: blue, yellow, or sometimes red, showy, with deep corolla tubes f. Bird Pollination i. Big red tubular flowers ii. Thin, high-energy nectar iii. Weak fragrance (birds are sight-feeders --- no sense of smell) g. Bat Pollination i. Night blooming ii. White iii. Robust iv. Often hanging below crown 4. Aggregate fruit from multiple carpels 5. Animal dispersal, passive 6. Explosive dispersal vi. Pollination Syndromes 1. Morphologically convergent adaptive trends exhibited by the floral features of pollinated plants and, in animal pollination, the mouthlike structure and other flower-interactive features of the pollinators

2. Passive a. Wind anemophily b. Water hydrophily 3. Active a. Animal zoophily 4. Caveats a. Not all visitors are pollinators b. i.e. robber hummingbird on Campsis c. Many plant species with a specific syndrome have surprising suite of effective pollinators vii. Why Do Animals Pollinate Plants? 1. Food reward a. In exchange for moving their pollen to another flower 2. Nectar a. A sugary solution produced in special flower glands called nectaries b. Nectar concentration matches energy requirement of the pollinator: bird- and bee- pollinated flowers have different sugar conc. 3. Pollen a. High in protein, some bees and beetles eat it b. Flowers sometimes produce two kinds of pollen: a normal and a sterile, but tasty, kind, for the insect V. Angiosperm Diversity A. Flower B. All of the majr structures are very different from the structures found in Gymnosperms C. How did they evolve? i. Parts of a flower are thought to be modified leaves ii. Development of flowers suggests that the parts of flowers are modified leaves

D. Pattern Formation in Plants: How to Make a Flower i. Four Flower Organs Whorl Structure in Flowers ii. Differences in gene expression in these whorls must give rise to different organs that make up the flower iii. Why use mutants? 1. Mutant phenotypes provide information about the biological role of the gene product in an organismal or cellular context (in vivo) by providing information concerning what goes wrong when the product does not function properly. 2. A cloned gene can provide biochemical information about its product a. Enzyme b. Transcription facotr c. Structural protein 3. Researchers need both phenotypic and biochemical information about their gene to understand its role 4. Identification of a gene by mutant phenotype = forward genetics 5. Using a cloned/mutated gene to find a mutant phenotype = reverse genetics iv. How do the proper flower parts form in the proper arrangement? 1. Genetic dissection used to identify genes required for proper floral organ identity 2. Scientists identified homeotic mutations that resulted in the misplacement of floral organs a. Homeotic genes Genes that determine the developmental fate of entire portions of an organisms v. Mutagenesis 1. Mutants are generated by exposing a population of organisms to a mutagen and allowing the individuals in the population to reproduce

a. Mutagens = irradation (e.g. UV, x-ray); chemicals (e.g. ethyl methane sulfonate) 2. Mutagen induces multiple mutations in the genome of the cells exposed (mutations are heterozygous in diploids) a. AA Aa b. In plant species that self fertilize, the next generation will include some plants homozygous for mutations 3. Grow many (1000s) of plants and look for the ones that are different in the character of interest 4. Identify the gene that has been mutated vi. Class A 1. Flowers with these mutations have unfused carpels instead of sepals in Whorl 1 and stamens instead of petals in Whorl 2 2. Pattern of organs (from outside to inside) is: a. Carpel, stamen, stamen, carpel vii. Class B 1. Flowers with these mutations have sepals instead of petals in Whorl 2 and unfused carpels instead of stamens in Whorl 3 2. Pattern of organs (from outside to inside) is: a. Sepal, sepal, carpel, carpel viii. Class C 1. Flowers with these mutations have petals instead of stamens in Whorl 3 and sepals instead of carpels in Whorl 4 2. Additionally, the floral meristem is not determinate flowers continue to form from within the flowers 3. Pattern of organs (from outside to inside) is: a. Sepal, petal, petal; sepal, petal, petal; sepal, petal, petal, etc.

ix. Each class of genes is required in two adjacent whorls: 1. Class A genes required in Whorls 1 and 2 2. Class B genes required in Whorls 2 and 3 3. Class C genes required in Whorls 3 and 4 4. *Differences in gene expression in these whorls must give rise to the different organs that make up the flower x. ABC genes have been identified as transcription factors 1. These genes regulate the transcription of other genes often in combination with other transcription factors VI. Plant Sex and Mating A. Sex and Mating i. Why do we care so much about reproductive biology? ii. Link to diversity 1. All kinds of ways zygotes can be formed 2. This generates diversity of other lie-history traits as well as species 3. Why does so much reproductive diversity exist? iii. Asexual Reproduction 1. Reproduction of genetically identical individuals from a single parent plant 2. Two main types: a. Vegetative reproduction (modes) i. Rhizomes (underground shoots) ii. Tillers (aboveground shoots) iii. Bulblets (little bulbs) iv. Bulbils (inflorescence veg buds) v. Cuttings b. Agamospermy i. Seeds w/o sex = production of seeds genetically identical to parent asexually, w/o fertilization between gametes ii. ~35 families, 130 genera, 400 species

iii. Obligative or facultative iv. May have evolved independently multiple times from sexual ancestors 1. E.g. Embryo sac = develops without mitosis (egg is diploid) 3. No meiosis, no fertilization and no recombination 4. Advantages of Asexual Reproduction a. Parent plants that are well-adapted to local environment will have offspring with a competitive advantage b. Less reproductive effect = e.g. less attraction and reward for pollinators c. Ability to colonize easily dont have to find mates d. Little if any new genetic variability e. Very narrow population niche width f. No dormancy and limited dispersal often iv. Sexual Reproduction 1. Production of offspring through meiosis and fertilization a. Offspring genetically different from parents due to recombination (genetic diversity) 2. Plants can be both sexual and asexual, with a variety of forms 3. Flowering plants are generally hermaphroditic v. Inbreeding Depression 1. Reduction in fitness of inbred offspring in comparison with outcrossed offspring 2. Manifested by reductions in viability and fertility 3. Genetic consequences (inbreeding) a. Genetic frequencies altered b. Allelic frequencies unchanged c. Heterozygosity reduced by 50% per generation d. Homozygosity for deleterious alleles gives inbreeding depression vi. Strategies to Prevent Self-Fertilization 1. Mechanism promoting outcrossing

2. Timing of male/female sexual phases 3. Spatial variation in female/male sexual phases 4. Genetic incompatibility VII. Plant Sex and Mating Cont.. A. Physical Separation of Reproductive Parts i. Unisexual flowers 1. Staminate and carpellate flowers ii. Monoecy 1. Separate male and female flowers, but on same plant iii. Dioecy 1. 6-7 % of angiosperms 2. Common in tropical regions and oceanic islands 3. Generally small flower size 4. 100% outcrossing, but inefficient 5. Sometimes controlled by sex chromosomes a. Silene 6. Separate male and female flowers, but on different plants iv. Herkogamy 1. Approach herkogamy a. Stigma above anthers very common 2. Reverse herkogamy a. Anthers above stigma b. Common in moth and butterfly pollination v. Distyly 1. 2 floral morphs 2. Thrum flower a. Long filaments w/short styles 3. Pin flower a. Short filaments w/long styles 4. Only pollinations between different floral morphs are successful vi. Tristyly 1. 3 floral morphs 2. Style long, stamens short and medium 3. Style medium, stamens short and long

4. Style short, stamens medium and long 5. Only 3 families! vii. Enantiostyly 1. Left-right separation 2. Cyanella alba viii. Flexistyly 1. Temporal separation 2. Alpinia B. Temporal Separation of Reproductive Parts i. Protandry 1. Anthers release pollen before stigma receptive 2. Common in insect-pollinated plants ii. Protogyny 1. Stigma receptive before pollen release 2. Less common than protandry C. Hermaphroditic Flowers i. Self-compatibile (SC) 1. Capable of self-fertilization or cross-fertilization 2. Often evolves from self-incompatibility a. Reverse is much rarer ii. Self-incompatible (SI) 1. Only capable of cross-fertilization 2. Inability of hermaphroditic plant to produce zygotes w/self-pollen 3. 40-60% of angiosperm species 4. Disadvantage = Relies on effective cross-pollination, seed dispersal and establishment 5. One of the most common transitions in flowering plant evolution is outcrossing to selfing (though not the reverse) D. Self-Pollination i. Self-fertilization ii. Pollen transfer within or among flowers of same individual

iii. ~20% of angiosperms are habitual selfers iv. Advantages 1. Reproductive assurance 2. Selectively advantageous by transmitting both sets of genes to offspring 3. Only single colonizing individual needed 4. Cost-saving on male expenditure v. Disadvantages 1. Decreases genetic variability 2. Inability to adapt to changing conditions 3. Inbreeding depression vi. Cleistogamy (CL) 1. Flowers never open and only capable of self-fertilization in bud 2. Inconspicuous, bud-like apetaous flowers that form directly into seed capsules 3. ~500 species

E. Identifying and Testing How Traits May Affect Species Diversity i. Angiosperms are most diverse group of plants on earth today 1. ~250,000 spp ii. Phylogenies tell us about the pattern of species diversification iii. Number of species present today in a clade is the product of both speciation and extinction iv. Diversification considers both simultaneously

v. Origin of flowers in the angiosperms is linked to origin of pollination vi. Does biotic pollination affect species diversification? vii. Evolution of nectar spurs provides increased opportunity to specialize on different pollinators 1. Prezygotic isolation may therefore be more likely to evolve in these groups viii. What kind of factors may influence the rate of species diversification? 1. Traits that increase the likelihood of evolving reproductive isolation 2. Prezygotic isolation a. Plants animal versus abiotic pollination b. Nectar spurs ability to specialize on pollinators c. Zygomorphic flowers 3. Risk of extinction a. Clades with self-pollination has very low speciation rates and likely go extinct quickly b. Outcross pollination promotes diversification

Introduction to Animals: Sponges VIII. Animal Diversity A. Why do we care? i. Diverse ecosystems are healthier ii. Ecosystems provide us with resources B. What Characters Distinguish Animals from Other Organisms? i. Multicellular organisms but incredibly diverse C. Nutritional Considerations: Heterotrophic Metabolism i. Animals must consume organic compounds ii. Lack ability to make them from inorganic molecules iii. Digest internally, somehow (this is in the highly variable in the animal kingdom) D. Feeding Strategies i. Filter feeders ii. Herbivores iii. Predators iv. Parasites v. Detritivores E. Some Sort of Motion is Required To get the Food i. Motion is relative 1. Locomote to get food 2. Move environment 3. Sit and wait ii. Energy is expended F. Body Symmetry i. Assymentrical 1. Body sponges ii. Radial Symmetry 1. Sea anemones iii. Biradial Symmetry 1. Fish 2. Humans G. Locomotion & The Need to Find Food Has Resulted in Unique Systems i. Sensory systems are unique as compared to plants, for example

1. Variety of sensory structures 2. Nervous systems to process and coordinate the sensory information and organize a response ii. Behavior 1. In this regard, animals are much more complex than plants H. With all this variety, how do biologists describe the evolutionary relationships among the animals? i. Look for common ancestor 1. Probably a colonial protest 2. Metazoan lineage is monophyletic 3. Choanoflagella links Protists and Animals a. Thought to be colonial and related to sponges I. Animal Evolutionary Relationships i. Phylogenies are estimates of relatedness ii. Can be made with morphological data or with molecular data iii. Many different approaches combined J. Monophyly Supported By i. Sequence similarities in 5S and 18S ribosomal RNAs ii. Sharing similarities in Hox genes iii. A series of special cell-cell interactions iv. A common set of extracellular matrix molecules such as collagen K. Phylum Porifera: The Sponges i. Sponges separated early in the animal lineage ii. Sponges are benthic, attach to the bottom substrate iii. Sessile (dont move) iv. Unique feeding system v. Cell types are key features vi. Pore bearer vii. Approx. 9000 living species viii. Three types: 1. Desmosponges 2. Glass sponges 3. Calcareous sponges ix. Multicellular 1. But lack tissue-level organization typical of other metazoans

2. Cells are totipotent (not differentiated and can alter form and function x. Lack symmetry (assymetrical) xi. Cellular organization is unusual xii. Ecology 1. Sessile Organisms 2. Suspension Feeders 3. Mostly benthic marine environments, with a few freshwater species 4. Occur at all depths L. General Sponge Body Plan i. Loose aggregation of cells surrounding a water canal system ii. No mouth iii. Unique feeding system based on bulk, one-way movement of water 1. Provides food, oxygen and a waste removal system 2. Can move incredible volumes of water iv. Specialized feeding cells: choanocytes 1. Move water into the animal v. Choanocytes filter food particles from the water as it moves by 1. Usually bacteria 2. Some species can pick up dissolved organic matter vi. Water exits via the osculum vii. Other amoebalike cells provide some rigidity viii. Spicules supporting spines 1. Not really a skeleton 2. Can be some fibers as

well M. Cell Diversity in Sponges i. Numerous cell types, plus spicules ii. Five significant varieties 1. Chaonocyte 2. Archaeocyte 3. Pinacocytes 4. Porocyte 5. Sclerocyte N. What Trends Will we Consider? i. Multicellularity ii. Cell Differentiation iii. Cell Specialization 1. Division of labor iv. Increasing Complexity 1. Organized tissue v. Behavior vi. Feeding strategies vii. Evolution of body plan viii. Cephalization ix. Skeletons of varying complexity and nature O. Choanocytes i. Central flagellum ii. Surrounded by a collar of microvilli iii. Collar is major site for absorption of nutrients iv. Phagocytosis and pinocytosis deliver nutrients to the mesophyll and other cells P. Feeding in Sponges: Intracellular Digestion i. Series of sieves collect food particles ii. Collar microvilli trap bacteria, large dissolved organic molecules iii. Particles moved by microvilli to base iv. Small particles are ingested by cell body via phagocytosis or pinocytosis v. Food vacuole passed onto archaoecytes

Q. Skeletal Support i. Spicules supporting spines 1. Not really a skeleton 2. Also can be some fibers as well ii. Spicules made of various materials 1. Calcium carbonate and silica 2. Others are made of an organic substance called spongin (proteinaceous) R. Sponge Diversity i. Incredibly diverse in color and shape ii. About 10,000 species world-wide iii. Predominantly marine 1. Except some freshwater a. Spongillidae iv. Found at all latitudes and in all marine environments from the deep-sea to the intertidal zone v. Body shape tends to correlate to habitat vi. *Body shape correlates to pattern of water movement S. Important Source of New Drugs i. Pharmaceuticals from marine invertebrates 1. Important argument for conversation of the worlds oceans ii. Marine biopropecting! iii. Example: 1. Great Barrier Reef in Australia a. Only ~5% if protected T. Natural Products from Sponges i. 14 sponge-derived compounds ii. Pacific sponges iii. Prianos spp. 1. Extract an alkaloid from sponges manzamines 2. Maybe produced by symbiotic bacteria 3. Treats malaria and TB iv. Halichondria okadai 1. Halichondrin B 2. Anti-melanoma and leukemia


Phylum Cnidaria A. Contains over 10,000 species i. Anthozoans: corals & sea anemones ii. Scyphozoans: Jellyfishes iii. Hydrozoans iv. Cubazoans B. Evolutionary Relationships i. Next split from the animal lineage after sponges ii. Most are marine iii. Most distinct changes: 1. Two embryonic cell layers 2. Distinct organ systems C. Features i. Basic radial symmetry ii. Only 2 layers of living tissue 1. Epidermis and gastrodermis iii. Middle gelatinous layer the mesoglea 1. In between the 2 living layers of tissue iv. Tentacles surrounding the mouth v. Only a single opening to the digestive system 1. Gastrovascular cavity 2. Blind gut vi. Nematocysts that account for the stinging activity that is associated with these animals. vii. Some swim, some dont viii. Simple carnivores ix. Very low metabolic rates 1. Can survive in cold and nutrient poor waters (polar) D. Body Plan i. Radial symmetry 1. Biradial 2. Quadriradial ii. Morphology of body 1. Body a. Blind gut

b. Radiating, non-centralized nerve net 2. Ring of tentacles a. Feeding b. Sensory structures iii. Gut with tentacles E. Multipurpose Cavity i. Gastrovascular cavity ii. Multiple purposes 1. Digestion 2. Gas exchange (no gills) 3. Circulation F. Cnidarian Physiology i. Gastrovascular cavity is region of gas exchange and digestion ii. Lack of a circulatory system 1. Gastrovascular cavity can be highly branched in large cnidarians iii. Extracellular Digestion 1. Cells in gastroderm contain digestive enzymes iv. Epithelial cells with muscle fibers that allow movement v. Diffusion based system G. Cnidarian Body Wall Crosssection i. Gastrovascular cavity (A) ii. Gastrodermis (B) iii. Mesoglea (C) iv. Cnidocysts (D) v. Epidermis integument (E) H. Cnidocytes (Stinging cells) i. Cells are at the end of tentacles ii. Eject a nematocyst iii. Threadbags iv. Can inject toxin into prey I. Advancement in the Nerves Department i. Unlike sponges, cnidarians have nerves and muscles ii. First animal (Metazoan) to have one iii. Not a true nervous system

iv. Mesh of overlapping decentralized nerves in a network J. Cnidarian Diversity i. Scyphozoans (jellyfish) 1. Jellyfish or G:cup animals 2. Thick mesoglea 3. Large, effective swimmers 4. All marine ii. Anthozoans (corals and anemones) 1. G: flower animals 2. Corals & sea anemones 3. Corals: reef building organisms iii. Hydrozoans 1. Contains only freshwater cnidarians + marine forms 2. Sessile forms and colonial swimmers 3. Freshwater hydrozoan Hydra 4. Obelia polyps iv. Cubazoans (box jellies) 1. Box jellyfish 2. Very toxic sting 3. Sea wasps of Australia, Chironex fleckeri a. Northern Australia b. Fairly fatally poison c. 3 meter tentacles 4. Carybdea marsupialis 5. Four tentacles 6. Have eyes K. Zooids i. Pneumatophore the sail ii. Dactylozooid 1. For defense 2. Fishing 3. 10 meters long and covered in nematocysts iii. Gastrozooid for feeding iv. Gonozooid reproduction

L. Coral i. Spatially dominant on coral reefs ii. Grow by vegetative propagation of polyps iii. Some also contain endosymbiotic photosynthetic dinoflagellates (zooxanthellae) iv. Tropical stony are critical to coral reef ecosystems 1. Reef builders 2. Calcium carbonate skeleton M. Symbiosis i. Marine symbiosis in cnidarians 1. Intra- and extracellular association with unicellular photosynthetic organisms 2. Gives cnidarians their green or brownish color ii. Marine cnidarians have dinoflagellates as endosymbionts (zooxanthellae) iii. Mutualism 1. Host obtains trophic benefits, nutritional benefits 2. Symbion gains shelter and access to sunlight iv. Coral-Zooxanthellae Symbiosis 1. Most reef-building corals normally contain a. 1-5 x 106 zppxanthellae/cm2 of live surface tissue b. > 1010 algal symbionts/m2 2. Relatively small biomass in relationship to their ecological effect = keystone species on coral reefs N. Coral Bleaching: Stress High Temperatures i. Loss of symbiotic zooxanthellae and/or a reduction in photosynthetic pigment in zooxanthellae residing within corals in termed coral bleaching ii. Zooxanthellae give coral their color, in their absence only the pale skeleton can be seen through the polyps transparent tissues iii. Coral bleaching is monitored 1. Degree heating weeks during mass bleaching in the tropical Pacific in 1998 iv. Marine biologists debate the nature of coral bleaching 1. Two schools, generally speaking:

a. Stress response b. Adaptive Bleaching Hypothesis (ABH) i. Premise: bleaching is a regulated mechanism that corals use to switch out symbionts in response to variable environmental conditions ii. High risk ecological opportunity O. Phylum Ctenophora i. Comb jellies ii. Very similar to cnidarians iii. Possess two openings to the gut (complete gut) iv. No nematocysts v. Feed with sticky ctenes or material on body vi. All marine and carnivorous vii. Possess eight rows of cilia-like projections ctenes X. Worms A. Two Major Animal Lineages i. Protostomes 1. Blastophore becomes the mouth 2. Spiral cleavage 3. Ventral nervous system 4. Freefloating larvae with complex cilia 5. Anterior brain ii. Deuterostomes 1. Blastophore becomes the anus 2. Radial cleavage 3. Dorsal nervous system 4. Larvae has feeding system with single cilium B. Protosomes Split into 2 Lineages i. Lophotrochozoans 1. Flatworms 2. Ribbon worms 3. Segmented worms ii. Ecdysozoans 1. Roundworms

C. Parasite i. Symbiuonts ii. Intimate & durable relationship iii. Parasite benefits at the hosts expense iv. A parasite feeds on a host without killing it v. Parasite Strategy 1. Reproduce within the host 2. Get fertilized eggs or embryos out of the host 3. Contact and recognize a new, correct host 4. Get entrance into the host 5. Locate the appropriate environment within the host 6. Hold on to the host 7. Withstand what is often an oxygen-poor environment 8. Avoid digestion or attack by the hosts immune system 9. Avoid killing the host, at least until developed to the appropriate life stage 10. Very efficient at converting food to energy D. Flatworm i. Flat most distinguishing characteristic ii. Simplest animals with bilateral symmetry iii. 25,000 species iv. Increasing in physiological and ecological complexivity v. Free-living and over-half are parasitic vi. Most are flukes and tapeworms vii. Tripoblastic 1. First group to evolve a true mesoderm viii. Aceolomates 1. Primitive or derived character? ix. Have a primitive gut 1. Some small free-living forms lack a gut 2. Lack an anus 3. One pharyngeal opening x. Lifestyle 1. Move around via cilia bands on ventral surface

2. Freshwater and marine 3. Complex life cycles 4. Often hermaphroditic 5. Free-living members are carnivores or scavengers on dead things 6. Most members are parasitic 7. Some cause important human and veterinary diseases xi. Anatomy 1. Diffusion is a significant force for these animals a. Respire by diffusion b. No cell too far froim the outside c. Flattened shape is a functional necessity d. High surface area to volume ratio 2. Can support an active lifestyle 3. Gut is blind and highly branches 4. No specialized respiratory or circulatory system xii. Cephilization & Sensory Capability 1. Eyespots are present 2. Other sensors a. Chemoreceptors b. Mechanoreceptors c. Statocysts 3. Primitive nervous system a. Distinct brain (central ganglion) with longitudinal nerve cords xiii. Diversity 1. Four classes a. Turbellaria i. Compromise only 16% of the phylum ii. Simplest flatworms

iii. Mostly free-living iv. Marine and freshwater v. Example: Planarians b. Trematoda i. The flukes ii. All parasites iii. Have a mouth and a blind gut iv. Ingest hosts blood and tissue v. Complex life-cycle vi. Cause significant world-wide diseases 1. Schistosomiasis estimates in 76 countries & 800,000 deaths/year c. Monogenea d. Cestoda i. All internal parasites ii. Vertebrate definitve host iii. Highly specialized for the parasitic lifestyle 1. No mouth or digestive tract 2. Greatly increased external surface area 3. Scolex: attachment structures a. Reproduction specialists 4. Proglottid a. Mature ones contain eggs b. Break off or burst in gut of host c. Eggs are shed in feces E. Ribbon Worms i. 900 species ii. Soft-bodied worms iii. Mostly marine 1. Few, freshwater, terrestrial, and parasites iv. Characteristics of Nemerteans 1. Unsegmented 2. Organism can be very long 3. Unlike flatworms, they have a complete gut and an anus

4. System of blood vessels (simplest of animal with circulatory system) 5. Recognized as simplest animal with true vascular system 6. Proboscis: specialized feeding organ a. Hollow feeding organ b. Ejected from the worm 7. Structure supports ecology a. Body wall musculature and the rhynchocoel act as a hydrostatic skeleton b. Some nemerteans are effective borrowers c. Mechanical advantages 8. Feeding a. Carnivores b. Proboscis is shot out of body c. Everts and secretes toxins that immobilize prey d. Muscous often secreted to help hold the prey e. Many feed on small invertebrates f. Some feed on eggs F. Segmented Worms i. 15,000 species ii. Ecologically diverse 1. Marine, freshwater, terrestrial iii. Carnivores iv. Anatomy 1. Bodies are a series of repeating segments 2. Ganglion controls each segment 3. Gas exchange across thin body wall a. Stays moist b. Restricted to moist environments 4. Circulatory system 5. Nephridia (little kidneys) 6. Muscles 7. True coelom

v. Defining Characteristics 1. One or more pair of chitinous setae per segment vi. Diversity: Four classes 1. Class Polychaeta a. Polychaete worms, mostly marine b. Exclusively marine worms c. 63% of annelids are polychaete worms d. Possess parapodia (distinctive thin, flattened outgrowths of the body wall; important role in polychaete identification; locomotion + highly vascularized; increased surface area) e. Burrowing polychaetes f. Male and female animals g. Release gametes 2. Class Oligochaeta a. Mostly freshwater, terrestrial b. Earthworm is in this class c. Only 6.5% are marine d. Example: common earthworm, Lumbricus

e. All hermaphroditic f. No parapodia, streamlined body g. Anterior end lacks conspicuous structures such as eyes h. No specialized respiratory structures i. Unlike polychaetes, very little body plan diversity 3. Class Hiurdinea a. Leeches b. 500-600 species, probably evolved from oligochaetes

c. Most are freshwater or terrestrial (reflecting the oligochaete ancestry) d. Defining characteristic = a posterior sucker e. Ectoparasitic, most commonly on blood of vertebrates f. 25% nonparasitic 4. Class Pogonophora a. Tube worms around deep-sea vents G. Phylum Nematoda i. About 16,200 species ii. Dioecious iii. Complete gut iv. Cuticle v. Molt cuticle to grow vi. Can have resistant stages vii. Many free-living species viii. Parasites of plants and animals ix. Ascaris lumbricoides 1. Human roundworm 2. Found worldwide 3. Infective stages in environment 4. Eggs can survive in formalin 5. Heavy infections can lead to malnutrition and bowel obstruction x. Heartworm in dogs and cats 1. Dirofilaria immitis 2. Mosquito bite transfers larvae to host 3. After development, juvenile worms migrate to the heart 4. Final maturation occurs in the pulmonary arteries, and the adult worms live in the right heart and pulmonary arteries for up to 7 years 5. Routinely lethal


Mollusks A. Four classes of mollusks i. Chitons 1. Mostly marine herbivores 2. Many plates 3. ~900 species 4. Common in intertidal zone 5. Restricted to living on hard substrata, especially rocks 6. Distinctive shell (8 overlapping, articulated plates) 7. Grazers 8. Girdle acts as a suction cup 9. Adaption for life in areas with heavy wave action (i.e. rocky intertidal zone) ii. Bivalves 1. Clams, scallops, oysters, mussels 2. 7,000 species 3. Freshwater and marine 4. Hinged shell with adductor muscles 5. Lateral compression of body and foot 6. Lack of cephalization (virtual absence of head and associated sensory structures) 7. Sedentary lifestyle 8. Absence of radula (gills for feeding) iii. Gastropods 1. Snails and slugs a. Pulmonate snails (lungs) b. Vascularized mantle cavity c. Land and freshwater d. Escargot 2. Aquatic and terrestrial 3. Largest gastropod class (~70,000 living species)

4. Visceral mass sitting atop a muscular foot 5. 90-180 torsion of visceral mass and nervous system during embryonic development 6. Operculum iv. Cephalopods 1. Squid and octopus 2. Exclusively marine 3. Fast moving, active carnivores 4. Complex behaviors 5. Extreme cephalization 6. Only Nautilus has an external shell 7. Octopus locomotion: bipedal locomotion with a hydrostatic skeleton 8. Chromatophores octopus and color change 9. Squid a. One of the largest fisheries in California b. Jet propulsion locomotion c. Vulnerable to predation due to loss of shell d. Photophores bioluminescence e. Chromatophores f. Squid mating orgies i. Odor in egg mops ii. Males pass sperm to females g. Vampire squid i. Deep sea specimen ii. Only member of the order Vampyromorphida iii. Unique retractable sensory filaments h. Architeuthis dux i. Giant squid ii. 18 m long, 2,000 pounds B. Features i. Body plan diversity is a highlight ii. Commonalities in body plan 1. Foot (used for locomotion or clinging)

2. Visceral mass (centralized organs) 3. Mantle (Dorsal epithelium forms mantle which secretes a calcareous shell) iii. Biodiversity iv. One of the relatively large animal phyla with ~100,000 living species (most gastropods) v. Dissimilar body shapes vi. Band of teeth (radula) used for feeding (missing in the bivalves) C. Body Plan i. Shell ii. Greatly reduced coelom iii. Complete digestive system iv. Open circulatory system (except in cephalopods) D. Unique Among Molluscans i. Closed circulatory system ii. Large differentiated brain 1. Behavior 2. Memory 3. Learning XII. Arthropods I A. Many zoologists describe arthropods as most successful animals i. Occupy land, sea, and air ii. Dominant in terms of species number at over 1 million iii. Also in terms of abundance: 1018 individuals B. Enormous diversity C. Defining characteristic = Epidermis produces a segmented, jointed and hardened chitinous exoskeleton D. Jointed appendages first appeared in trilobites i. Extinct marine arthropod ii. Diagnostic features of Paleozoic Era iii. Went extinct in a catastrophic event that removed an estimated 90% of all species on Earth

iv. Extensive fossil record because hard parts fossilized well v. Estimated 10,000 species with considerable ecological diversity E. Why are they so successful? i. Rigid exoskeleton 1. Multilayered structure a. Contains protein, calcium and chitin complexed together 2. Chitin, a polymer (polysaccharide) 3. Rigid a. Provides protection b. Surface for muscle attachment 4. Had significant impact on arthropod evolution a. Physical stability from the exoskeleton supports walking on dry land b. Chitinous nature adds waterproofing reduces evaporative water loss on land c. Predisposed aquatic arthropods to invade the terrestrial environment 5. Also considered a barrier to growth a. Molting, ecdysis b. Under hormonal and neuronal control i. Y-organ produces ecdysteriod hormone c. Old cuticle is partially digested by enzymes d. Split by water, air or elevated blood pressure (body swells) ii. Segmentation 1. Body divided into segments 2. Jointed appendages on different segments 3. Moved by attached muscles 4. Appendages support complex locomotion a. Walking b. Swimming c. Flight 5. Other functions

a. Facilitates prey capture b. Supports sensory perception iii. Jointed appendages 1. Appendages modified for different functions 2. Specialization is major theme in arthropod evolution F. Functional Features of Arthropods i. Muscles: Striated, unlike muscles in most other invertebrates which are smooth ii. Circulatory System 1. Open circulatory system 2. Heart plus a few major arteries 3. Returning blood spills into body cavity (hemocoel) and enters heart via ostia (diagnostic for arthropods) 4. Respiration is more variable a. Gills, trachea and spiracles 5. Hemocyanin, copper-containing oxygen-carrying protein in blood iii. Nervous System: increasingly advanced 1. Brain 2. Muscular control 3. Compound eyes iv. Respiratory System 1. Trachea: improved gas exchange 2. Book lungs in spiders G. Diversity i. Phylum Crustacea 1. 67,000 species world-wide 2. Dominant marine arthropods 3. Distinguishing Characteristics a. Body divided into 3 regions: head, thorax, and abdomen b. Carapace c. Naupliud larvae d. Chromatophores i. Under neurohormonal control

ii. Body color changes in crustaceans iii. Used as camouflage in nature 4. Decapods (lobsters, crabs, shrimp) 5. Isopods (sow bugs, terrestrial) a. Many marine species b. Most successful crustacean that invaded land c. Sow bugs and pillbugs 6. Amphipods (sand fleas) 7. Copepods a. Predatory and planktonic b. May be the most abundant animal on the plant c. Zooplankton food web d. Production of fecal pellets produces marine snow 8. Barnacles a. Semibalanus balanoides is an obligate cross-fertilizing hermaphrodite b. Barnacle penis is much longer than the body c. During the reproductive season, penis searches an area around the adult to find a receptive functional female d. After copulation, the penis degenerates and is regrown the next year ii. Phylum Hexapoda (insects) iii. Phylum Myriapoda (e.g. centipedes) iv. Phylum Chelicerata (spiders) XIII. Arthropods II A. New Medium i. Advantages 1. Air much less viscous as compared to water (Animal locomotion approaches some serious speeds) 2. Much more oxygen water has 5 ml/l and air can have 210 ml O2/l total air

3. Oxygen delivery to tissue is better in air environments ii. Disadvantages 1. Density air is less dense (water is 1000x more dense) must design robust skeletons 2. Temperature thermal capacity is much higher - means very rapid change in temperature in air B. Hexapoda 6 legs i. Insects, six legged arthropods ii. Over 1 million species iii. First animals to evolve flight iv. Extremely successful in transition to land v. Most are terrestrial 1. Some aquatic for part or all of lifecycle 2. No marine insects C. Insects: The Dominant Arthropod i. Body divided into head, thorax, and abdomen ii. Three pairs of appendages on the thorax iii. Possess trachea used in gas exchange with the environment 1. Key feature that allows enormous radiation of uniramians into terrestrial habitats 2. Maximimizes body surface area over which respiratory gas exchange can occur iv. Respiratory system is a great advantage in the dry, terrestrial environment D. Unique Respiratory Gas Exchange System in Insects i. Internal system ii. System of highly branches air filled tubes called trachea iii. Branch throughout the insects body to reduce diffusion distance E. Spiracles are openings on the exterior surface of the animal for gas exchange

Winged and Wingless Insects i. Wingless 1. Relative to insects a. Silverfish b. Springtails 2. Simple development a. Juveniles look like adults once hatched from egg ii. Winged 1. Pterygote insects 2. Origin of insect wings a. Developmental genes, pdm/nubbin b. Gene expression data c. Antibodies vs. Pdm/nub protein 3. How did flight evolve? a. Ancestor most likely a centipede-like aquatic animal b. Insect wings originated from the gill of the ancestral aquatic arthropod during transition to land 4. Ecologically successful a. Could avoid predators b. New habitats = new food sources c. Could barriers to dispersal 5. Complex systematics (28 orders) 6. Complex development a. Larval forms dont look like miniature adults b. Numerous instars 7. Three groups: a. Cannot fold wings against body b. Can fold wings but undergo incomplete metamorphosis i. Orthoptera (grasshoppers, crickets, roaches, and walking sticks) ii. Isoptera (termites)

iii. Homoptera (aphids) iv. Dermaptera (earwigs) c. Can fold wings and undergo complete metamorphosis i. Most of the winged insects (~85%) ii. Larval and adult forms differ significantly 1. Larvae feed and grow 2. Adults reproduction and dispersal iii. Familiar orders 1. Coleoptera (beetles) 2. Lepidoptera ( butterflies and moths) 3. Diptera (flies) 4. Hymenoptera (bees, wasps and ants) F. Odontata i. Dragonflies and damselflies ii. Only member of the first group on last slide (pterygote insects) iii. Aquatic larvae that metamorphose out of the water iv. Predators G. Chelicerates i. Scorpions, spiders, mites, horseshoe crabs, and sea spiders ii. Distinct body regions: an abdomen and a cephalothorax 1. Anterior where appendages are modified to form mouth parts the chelicerae- clawed for grabbing and shredding food 2. Rest of body has 4 pairs of walking legs 3. Lack mandibles near the mouth H. Class Pycnogonida i. Sea spiders ii. All are marine 1. ~1000 species iii. Most are small bodied, legs much longer then the body iv. Complete digestive system with sucking mouth part v. No specialized respiratory or excretory system I. Arachnids

i. 70000 living arachnid species ii. Spiders, mites, ticks, and scorpions iii. 50% are spiders 1. Chelicerae modified into fangs with associated poison glands 2. All spiders are predators 3. Have 4 pairs of walking legs 4. Most spiders have special silk glands which produce silk 5. Have simple eyes (better at detecting motion) 6. Use book lungs for gas exchange 7. Book lungs a. Found in primitive spiders b. First respiratory system c. Consists of a stack of plates d. Blood flows through these plates and the gas is exchanged iv. Mostly terrestrial, although ancestor was marine J. Merostomata i. Horseshoe crabs, only 4 species ii. An acient species iii. Limulus amoebocyte lysate assay to test for endotoxin, a substance commonly associated with many symptoms caused by bacterial infections in humans iv. Mass spawnings K. Myriapods i. Body plan: two regions instead of three: head and trunk ii. Centipedes 1. One pair of legs/ segment 2. Carnivorous iii. Millipedes 1. Two pairs of legs/segment 2. Scavengers, consume plants as well XIV. Introduction to Deuterostomes & Echinoderms A. Deuterostomes i. Contain the echinoderms, hemichordates, and chordates ii. Many organisms of great importance to ecosystems

iii. Complex relationships with humans 1. Agriculture 2. Fishing 3. Medicine iv. Three main clades: 1. Echinoderms 2. Hemichordates 3. Chordates v. Phylogeny 1. Many evolutionary parallels with the protostomates a. Ecological i. Both colonized land ii. Food sources: filter-feeding, food in sediments or on surfaces b. Anatomical/structural i. Compartmentalization of body ii. Feeding appendages iii. Mechanisms to move water for feeding iv. Planktonic feeding larval stages B. Echinoderms i. G: spine skin ii. ~7,000 species iii. Strictly marine iv. Many more forms found in the fossil record v. Calcified internal system vi. Water vascular system 1. Series of fluidfilled canals 2. Connected to numerous feeding and locomotory appendages, the tube feet 3. 5-pointed radial symmetry in

adults (not larvae) a. Larvae are bilaterally symmetrical vii. Spacious coelom viii. Complete gut (usually) ix. Generally lack respiratory systems x. Only rudimentary circulatory systems xi. Water vascular takes over many of these functions 1. Linked to seawater via the sieve plate 2. Strong canal connects to the ring canal 3. Radial canals (5) radiate from the ring canal 4. Bulbs connected to all tube feet a. Protrude between the plates b. Have suckers at the end c. Extended by hydraulics d. Retracted by contraction of longitudinal muscles e. Used for locomotion and feeding f. Average number is 2,000 tube feet per animal xii. Poorly developed nervous system xiii. Internal Skeleton 1. Well-developed 2. ~95% calcium carbonate 3. Components of the skeleton are synthesized in specialized cells that originate from the embryonic mesoderm 4. Different from molluscan shell where minerals are deposited in a protein matrix C. Pycnopodia i. Pycnopodia helianthoides ii. 24 arms iii. Sunflower star may have 15,000 tube feet iv. Speedster @ 1 meter per min D. Echinoderm Diversity i. Two large subphyla (with different number of arms and variable water vascular systems) 1. Pelmatozoa (the Crinoids)

2. Eleutherozoa (several groups sea urchins, sea stars, brittle stars) ii. Other echinoderm groups (mobile) 1. Echonozoans (sea urchins and sand dollars, sea cucumbers) 2. Asterozoans (Sea stars and brittle stars) E. Class Crinoidea i. The Crinoids 1. Sea lilies and feather stars ii. Only 80 extant species iii. Sessile iv. Feeding mechanism 1. Pinnules and tube feet act as an adhesive fiber filter 2. Food particles moved into groove in arm a. Conveyor belted via ciliary action to mouth 3. Mucous secreted in some species F. Class Echnioidea i. Sea urchins and sand dollars 1. Lack arms but have 5-part radial symmetry 2. Grazers 3. Red urchins: important California fishery 4. Purple urchin genome sequencing project ii. *Aristotles Lantern 1. Specialized feeding structure around the esophagus 2. Composed of hard parts (ossicles) and muscle 3. Used to scrape and capture prey iii. Ecological role of sea urchins as grazers 1. Over-grazing? a. Urchin barrens created by the green sea urchins below 2. Insufficient grazing? a. The Green Reef G. Class Holothuroidea i. Sea cucumbers 1. Calcareous occicles are greatly reduced and embedded in body wall

2. Very worm shaped 3. Tentacles: the tube feet are modified 4. No cephalization 5. Evisceration a. Expulsion of GI tract through the anus b. Defense or seasonal atrophy? c. Usually regenerate d. Substance use of evisceration and regeneration in the Pacific Islands H. Class Asteroidea i. Sea Stars ii. Tube feet iii. Predators iv. Regeneration 1. Surgically bisected larvae: 12-14 days to regenerate 2. One gene, srap, was expressed at wound healing site 3. Related to plasmin v. Feeding 1. Everts stomach onto or into prey 2. Secrete digestive enzymes 3. Digested material reabsorbed by stomach into the body I. Other Classes i. Class Ophiuroidea 1. Brittle stars ii. Class Concentricycloidea 1. Sand dollars XV. XVI. Phylum Chordata Vertebrates A. Major Trends i. Invasion of sea, land and air ii. Aquatic and terresztrial forms 1. New forms of locomotion iii. Different reproductive strategies 1. Evolution of internal fertilization 2. Viviparous animals

iv. Eat large prey items jaws and teeth v. Evolved true powered flight B. Major Characteristics i. Dorsal nervous system ii. Internal skeleton iii. Vertebral column iv. Organs in a coelom v. Circulatory system C. What Makes a Vertebrate a Vertebrate? i. Chordates with a spinal column 1. Attaching muscles to internal frame ii. Vertebrates differ from other chordates 1. Vertebral column 2. Head (craniate chordates) iii. Others 1. Neural crest 2. Internal organs 3. Endoskeleton D. Evolution of Jaws i. First occurs in placoderms ii. Modification of anterior gill arches E. Devonian, the Age of the Fishes i. Placoderms 1. Early jawed fishes 2. Now extinct 3. Heavily armored ii. Other fishes evolved during this era: 1. Cartilaginous fishes 2. Ray-finned fishes 3. Lobe-ray fishes F. Class Chondrichthyes i. Evolution of jaws ii. Cartilaginous fishes 1. Skates, rays, sharks and chimaeras

iii. Increased mobility 1. No armor as in the placoderms 2. Fins (2 pair pectoral and pelvic) iv. Ancient lineage v. Skeleton is composed of cartilage vi. Lack true bone, except teeth may be calcified G. Class Osteichthys i. Ray-finned fishes ii. Evolutionary novelty 1. Swim bladder 2. Internal skeleton is bone, a living tissue iii. Ecology 1. Freshwater species 2. Marine 3. Estuarine 4. Salmon (transition during lifetime) H. Swim Bladder: Ecologically Significant for Fish i. Early bony fishes evolved this sac structure to aid in respiration ii. Supplemented gills iii. Good for hypoxic environments iv. In most modern bony fishes, now solely a buoyancy organs 1. Neutral buoyancy 2. Also aids in hearing underwater and sound generation v. Sharks have no swim bladder I. Life on Land: Evolution of the Tetrapods i. Ancestral form? 1. Lungfish-like animal 2. Exploited new food? 3. Most likely had a jointed fin to aid locomotion on land J. How Did Vertebrates Colonize the Land? i. Ancestor had jointed appendages 1. Coelocanths 2. Lungfish ii. Swim bladder-like structure was using a primitive lung

K. Tetrapods: 4 Major Classes i. Class Amphibia 1. Most basal of the tetrapods 2. Double life 3. Breath through skin and lungs in some species 4. Always connected to water 5. Challenges in move to land a. Water loss i. Dessication of body ii. Must reproduce in a xeric environment b. Adaptions i. Amniote egg ii. Water-tight skin iii. Kidneys that can concentrate urine ii. Class Reptilia iii. Class Aves 1. Evolved from the dinosaur lineage 2. Evolved specializations for flight a. Feathers b. Light hollow bones c. One-way breathing system d. Powerful flight muscles attached to breastbone 3. Radiation into numerous habitats a. Diving b. Aquatic forms c. Birds that have lost flight 4. How did flight evolve? a. Scales modified to feather b. Fantastic example of convergent evolution i. Bats, birds, dinosaurs ii. Excellent examples of transitional forms in the fossil record c. Flight stroke that matters d. Ground up hypothesis i. Strong predator escape mechanism (fly up)

e. Trees down hypothesis i. Strong predation mechanism (swoop down) f. Feathers are insulation? g. Why? i. Escape predators ii. Catch new prey iii. Free hind legs as weapons iv. Dispersal (move from place to place) iv. Class Mammalia 1. Ancestor: a mammal-like reptile 2. Warm-blooded=homeothermy 3. Features a. Mammary glands b. Sweat glands c. Hair d. Four-chambered heart 4. Four major groups of mammals a. Eutheria i. Placental mammals ii. Familiar examples. b. Marsupials i. Pouched animals ii. Kangaroos, oppossums, Tasmanian devils c. Monotremes i. Egg-laying mammals ii. Platypus iii. Have hair, produce milk, warm-blooded d. Marine Mammals i. Secondary invaders of the sea