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Home , Subphylum

2 Dr. Tim Revell SI: Claire Suh TA: Bryan Quintero Welcome to Bio 2! • Plant and Animal Interactions • Second Semester Majors Course • A course on , Biodiversity, Ecology, Conservation, Comparative Anatomy and Physiology • What have you heard??? • Powerpoint – Notes – Coming to – Camera! – Everything in the powerpoints is fair 2/17/14game for lecture quizzes/exams! 2 Class Expectations • No Cell Phones (talking or texting)! • No Cheating, stealing, or other behaviors deemed unethical • Be On Time; Be Awake; Be present! • Participate • Grades/Letters of Rec • Questions?

2/17/14 3 Carl Linneaus q Father of “______Taxonomy ” q Swedish botanist, physician, and zoologist q Wrote Systema Naturae in 1735 q The science concerned with naming and classifying the diverse forms of

• Bacteria: • Group: Proteobacteria Fungi: • ex: Salmonella, E. Coli : Chytridiomycota • Group: Gram (+) Bacteria Division: Zygomycota (Zygomycetes) • ex: Clostridium, Bacillus Anthracis, Division: Glomeromycota Streptococcus, Staphylococcus Division: • Group: Cyanobacteria Division: Basidiomycota • ex: Oscillatoria Division: Deuteromycota • Group: Spirochetes • ex: Treponema pallidum, Kingdom Plantae • Borrelia burgdorferi Division: Hepatophyta (liverworts) • Group: Chlamydias Division: Anthocerophyta (hornworts) • ex: Chlamydia Division: Bryophyta (Mosses) • Division: Lycophyta (Club Mosses) • Doman Archaea: Division: Pterophyta • Group: Methanogens * Psilophyta (Whisk ) • Group: Halophiles * Sphenophyta (Horse Tails) • Group: ThermophilesDomain Eukarya, Kingdom Protista Division: Pterophyta (Ferns) Division: Ginkgophyta • Supergroup: Excavata Division: Cycadophyta • Clade: Diplomonads Division: Gnetophyta • Clade: Parabasalids Division: Coniferophyta • Clade: Euglenozoans Division: Anthophyta • Group: Euglenids

• Group: Kinetoplastids Kingdom Animalia • Supergroup: Chromalveolatas (Lophophorate Phyla) • Clade: Alveolatas : Bryozoa • Group: Dinoflagellates Phylum: Phoronida • Group: Apicomplexans Phylum: Brachiopoda • Group: Ciliates Phylum Porifera • Clade: Stramenopila Class: Calcarea • Group: Bacillariophyta Class: Hexactinellidae • Group: Phaeophyta Class: Demospongiae • Group: Chrysophyta Phylum Cnidaria • Group: Oomycota Class: Hydrozoa • Supergroup: Rhizaria Class: Scyphozoa (Jellies) • Group: Foraminiferans Class: Anthozoa • Group: Radiolarians Class: Cubozoa (Box Jellies) • Supergroup: Archaeplastida Phylum Ctenophora (Comb Jellies) Phylum Platyhelminthes (Flatworms) • Group: Rhodophyta Class: Tubellaria • Group: Chlorophyta Class: Monogenea • Supergroup: Unikonta Class: Trematoda • Clade: Amoebozoans Class: Cestoidea • Group: Slime molds Phylum Rotifera • Group: Gymnamoebas Phylum Nemertea (Ribbon Worms) • Group: Entamoebas Phylum Nematoda (Round Worms) • Clade: Opisthokonts Phylum Mollusca • Group: Nucleariids Class: Monoplacophora • Group: Choanoflagellate Class: Polyplacophora Class: Gastropoda Class: Scaphopoda Class: Bivalvia Class: Cephalopoda

Phylum Chordata Phylum Annedlida : Urochordata () Class: Oligochaeta Subphylum: Cephalochordata () Class: Polychaeta Subphylum: Vertebrata Superclass: Agnatha (lampreys/hagfish) Class: Hirudinea Superclass: Phylum Onychophora Class: Chondrichthyes Phylum Arthropoda Class: Osteichthyes Subphylum: Trilobita Superorder: Ostariophysi Subphylum: Superorder: Procantheropterygii Superorder: Acantheropterygii Class: Merostomata Class: Amphibians Class: Pycogonida : Urodela (Salamanders) Class: Arachnida Order: Anurans (Frogs/Toads) Subphylum: Crustacea Order: Apodans (Caecillians) Class: Crustacea Reptiles Class: Testudines (Turtles/Tortoises) Subphylum: / Class: Sphenodontia (Tuataras) Class: Chilopoda Class: Squamata (Lizards/Snakes) Class: Diplopoda Class: Crocodilia Subphylum: Hexapoda Class: Dinosauria Class: Insecta Order: Omithiscians Order: Sauriscians Phylum Echinodermata Class: Aves Class: Asteroidea Order: Passeriformes Class: Ophiuroidea Order: Anseriformes Class: Echinodea Order: Columbiformes Class: Holothuroidea Class: Mammalia Order: Monotremata Class: Cnnoidea Order: Marsupialia Superorder: Eutheria Order: Artiodactyla Order: Perissodactyla Order: Rodentia Order: Carnivora Order: Sirenia Order: Cetaceans Order: Insectivora Order: Lagomorpha Order: Probocidea Order: Chiroptera Order: Edentata

Many different “systems” or “styles” for classifying life….

8 Cladistics

• ______Cladogram – A type of chart showing the relationship of the different groups to one another. • Clade – Any grouping on a cladogram that includes all of the descendents and a common ancestor. • Sister Taxa Cladistics • Shared ancestral characters – ______Plesiomorphies • Shared derived characters – ______Synapomorphies Cladistics • Outgroups – a clade () closely related to the ingroup but less closely related than any of the ingroup members. • Ingroups – The group we are trying to determine the relationships for. • The Law of Parisimony (Occam’s Razor) Cladistics Groupings • Monophyletic______– Clade that includes ancestor and all of its descendants. • ______Paraphyletic – Clade that includes ancestor and some, but not all, of it’s descendants. • ______Polyphyletic – Grouping that lacks a most recent common ancestor. 2/17/14 13 Domain: Bacteria Domain: Archeae Domain: Eukaryote Bacteria - Prokaryotes Bacteria Characteristics

• Nucleoid Region • Plasma – single circular membrane chromosome • Cell wall – plasmids ______– peptidoglycan • No membrane- • Capsule bound – glycocalyx organelles • Flagella • Ribosomes • Pilli (70S) • Fimbrae

Classification

• Shape (Cocci or Rod) • Staining – Gram – Spore – Acid-fast • Oxygen requirements • Feeding strategies Shapes

• Sperical (Cocci) • Rod-Shaped (Bacillus) • Spiral (Spirochetes)

2/17/14 19 Shapes and Groups Cocci: Spherical Strep_____ – in lines Staph_____ – in grape like clusters Shape

Helical: Spiral- shaped (Spirillium) Shape

Filamentous

Gram Stain • Bacteria are stained with a violet dye and iodine • Rinsed in Alcohol (Gram + retain violet dye, Gram - decolorize) • Stained again with a red dye • Results – Violet = gram positive – Red = gram negative

Know these steps!

Lab Acid-fast Stain

– Mycobacterium leprae, M. tuberculosis (Acid-Fast + Red, Negative Blue) 2/17/14 28 Spore Stain Oxygen Requirements • Obligate aerobes – require oxygen • Obligate anaerobes – require no oxygen • ______–Facultative anaerobe can grow with or without oxygen • Aerotolerant Anaerobes – only anaerobic growth but oxygen does not harm. • ______–Microaerophiles aerobic growth in low oxygen concentrations. Make sure you know this figure! Good Essay Question!!! Feeding Strategies

• Based on energy and carbon sources – Photoautotrophs – Chemoautotrophs – Photoheterotrophs – Chemoheterotrophs Feeding Strategies

Good essay Question! Nitrogen Metabolism

• Nitrogen is needed proteins/ nucleic acids • Nitrogen fixation - convert atmospheric N into ammonia • Makes N available for other organisms Which tree is most parsimonious?

Phylogeny of Prokaryotes 5 Groups of Bacteria Domain: Bacteria • Group:Proteobacteria – Salmonella • bacillus shape, gram negative, facultative anaerobe • Diarrhea, nausea – (chicken and reptiles) • Endotoxin – caused by cell wall Domain: Bacteria

• Group: Proteobacteria – E. coli • bacillus shape, gram negative, facultative anaerobe • Diarrhea • Exotoxin – releases proteins that cause illness Domain: Bacteria • Group: Gram-positive bacteria – Clostridium • Bacillus shape • endospore • Obligate anaerobes - exotoxins • Causes gangrene, ______Botulism (strongest poison in the world! – 1 gram can kill 1 million people!) Domain: • Group: Gram- Bacteria positive bacteria – Bacillus anthracis • Bacillus shape (endospore) • Aerobic • Causes pustules, pneumonia Domain: Bacteria • Group: Gram- positive bacteria – Streptococcus • Coccus shape & gram positive, anaerobic but are air tolerant • necrotizing fasciitis, strep throat, scarlet fever • Group: Gram-positive Domain: bacteria Bacteria – Staphylococcus, MRSA • coccus shape & gram positive, facultative anaerobe • Most common type of food poisoning, toxic shock syndrome • Dangerous in hospitals (______Nosocimal infections) • Iatrogenic

• Group: Cyanobacteria Domain: – Contains Chlorophyll A Bacteria and phycocyanin • Only organism on planet that can fix nitrogen and release oxygen • pools Domain: Bacteria

• Group: Spirochetes – Treponema______pallidum • Syphilis • anaerobic – Borrelia______burgdorferi • Lyme Disease • Microaerophile • zoonosis Domain: Bacteria • Group: Chlamydias – Chlamydia • coccus shape & gram negative • Causes blindness and is one of the most common STD’s in U.S. • Oxygen requirement uncertain Data: The Fossil Record

2/17/14 48 Fossil Record • ______Sedimentary • Hard Parts – most Rocks – type of rock likely to be that usually makes preserved as fossils best fossils

2/17/14 49 Fossil Record

• Organic Material • Minerals – when part of the replacing organic organism remains material

2/17/14 50 Fossil Record • Casts – • Trace Fossils – impressions made footprints, burrows, or by an organism other signs of activity

2/17/14 51 Fossil Record • Entire Organisms

2/17/14 52 Limitations of the Fossil Record • Habitat Bias – some habitat betters than others at making fossils • Slow Decay – Some organisms decompose too quickly or get destroyed before fossilizing • Temporal Bias – Time in which they lived and time of year. • Common Bias – More common animals are more likely to fossilize if events are rare and somewhat random

2/17/14 53 Dating Fossils Absolute Dating (half-life)

Carbon -14 5,600 years

Carbon -14 5,600 years

2/17/14 54 Relative Dating

2/17/14 55 Data:

Old Rock – Sea Geology New Rock – Sea floor Disappearing floor spreading

2/17/14 56 Data: Geology

• Pangaea (245 mya) • Pangaea began to break up (180 mya) – ______Laurasia (North) – ______Gondwana (South)

2/17/14 57 Geological Time Scale Know!!! This will be on the exam for sure!

2/17/14 58 Data: Anatomy

- Using similarities and differences (two kinds of similarities): - ______Homology - likeness attributed to shared ancestry Data: Anatomy ______Analogy - likeness due to similar ecological roles and natural selection due to convergent evolution

Data: Molecular Comparisons Molecular Homologies– Comparing various molecules of different organisms. Many ways to do this…(Pg. 29 for example) Data: Molecules as “clocks”

• Kimura, King • Neutral Theory • Molecular Clocks

2/17/14 62 Phylograms Length of a branch reflects the number of changes that have taken place in a particular DNA sequence in that lineage. Normal “Cladograms do not really tell you how much change has occurred Ultrametric Trees

Similar to a phylogram but all the branches that can be traced from the common ancestor to the present are of equal length. They do not imply evolutionary rates, but, they can place certain branching points in geological time. Bio 1/Ecology 1

• Bio 1 (or Bio 4) – All livings are made of cells – All livings come from other living things – All livings require energy to maintain homeostasis – All livings evolve – All livings things are part of other living things (Ecology)

2/17/14 65 Microevolution

• Small genetic changes in a population over time • ______Charles Darwin – The Origin of Species (1859) • Evolution by the process of natural selection

2/17/14 66 Microevolution

• Natural Selection – Differential success in the reproduction of different phenotypes (or genes) resulting from the interaction of organisms (populations) with their environment.

Make sure you know what this means…

2/17/14 67 How it works? • You start with a population (a group of species capable of reproducing) • There is variation in the population • The variation is a result of genetic inheritance • Some genes (traits) are better suited for survival and reproduction. • Those genes are passed on at a greater frequency than less desirable genes. • Over time, the genetic frequency of the population changes over time. Most of the time – bacteria…they can make a 2/17/14mess of this! 68 Microevolution

• Adaptation – An accumulation of inherited characteristics that enhance organisms’ ability to survive and reproduce in specific environments • …Now…Read Spandrel’s…

2/17/14 69 Evolution & Natural Selection

MRSA Example: X X X Day 1 X XX X X X X X X X X X X X X Day 2 X X X

X Day 3 X X 80 beak depthPeter and Rosemary Grant Microevolution1976 60

40

Average 20 beak depth, 1976 Average Number Number of individuals 1978 beak depth, 1978 0 5 6 7 8 9 10 11 12 13 14 Beak depth (mm) Shift of average beak 2/17/14 depth during drought 72 Two Patterns of Evolutionary Change

• Anagenesis – accumulation of heritable changes, altering the characteristics of a species • Cladogenesis______– the splitting of a gene pool into two or more separate gene pools resulting in new species.

2/17/14 73 Types of Speciation

• ______–Allopatric Speciation “Another Place” • ______Sympatric Speciation – “Same Place”

2/17/14 74 Allopatric Speciation – Favorable Conditions

• 1. Small Population • 2. Isolation • 3. Different Environment al Conditions

2/17/14 75 Allopatric Speciation

2/17/14 76 Sympatric Speciation

• Polyploidy ______Autopolyploidy (one individual involved)

2/17/14 77 Sympatric Speciation

• Polyploidy Allopolyploidy (more than one individual)

Oats, Cotton, Potatoes, Tobacco, Wheat (allohexaploid!) are all polyploids!)78 Adaptive Radiation

Emergence of many new species from a common ancestor. Usually occurs when many unexploited niches are available.

2/17/14 79 Macroevolution: Large genetic changes in a group over time (resulting in new species or new groups)

2/17/14 80 ______Gradualism • Also called “Neodarwinism” • Small changes over time accumulated over time • Supporter: Ernst Mayr

2/17/14 81 ______Punctuated Equilibrium • Supporters: Eldredge & Gould • Speciation occurs in episodic events: large periods = little change and short periods = large changes

2/17/14 82 2/17/14 83 Novelties may be versions of older structures Exaptation______- preadaptation

2/17/14 84 Hox Genes

2/17/14 85 Changes in rate and timing ______Paedeomorphosis - retention of juvenile features in an adult

2/17/14 86 Changes in rate and timing ______Paedeogenesis - sexual maturity in a larval

2/17/14 87 Investigating the Tree of Life

• ______Phylogeny – the evolutionary history of a species or group of species • ______Systematics – an analytical approach to understanding the diversity and relationship of organisms “ ______Ontogeny Recapitulates Phylogeny ” (Ernst Haeckel)

• Ontogeny – individual development • Recapitulates – repeats • Phylogeny – evolutionary descent Basic Idea – Animals that are closely related have similar developmental pathways. Classical Evolutionary Systematics

• George Gaylord Simpson Cladistics Groupings • Monophyletic______– Clade that includes ancestor and all of its descendants. • ______Paraphyletic – Clade that includes ancestor and some, but not all, of it’s descendants. • ______Polyphyletic – Grouping that lacks a most recent common ancestor. Comparing the genes or genomes of two species is the most direct measure of inheritance from shared ancestors. Comparisons can be made by using three methods: DNA-DNA hybridization, restriction maps, and DNA sequencing. Use the information to determine where species A through F belong in the phylogenetic tree. The information below is comparing the number of differences between an amino acid sequence from a blood protein found in rodents. (Assumption: The larger the number, the longer they have been separated from their common ancestor) A B C D E F A 0 10 4 9 14 10 B 10 0 11 5 16 2 C 4 11 0 10 15 10 D 9 5 10 0 15 6 E 14 16 15 15 0 16 F 10 2 10 6 16 0 Cladogram Place the taxa (outgroup, A, B, C, and D) on the cladogram based on the presence or absence of the characters 1-4 as shown in this table. Indicate before each branch point, which shared derived character evolved in the ancestor of the clade.