BILD 3 Midterm 2: Speciation & Origin of Life

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  1. Clade (definition)
    A single species & all of its descendants
  2. Monophyletic Group
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    • Consists of ancestor species and ALL of its descendants
    • Creates a valid clade
    • ex. If first common ancestor is MAMMAL, then all the rest would have characteristics of a MAMMAL
    • ex. Mammalia, aves (birds), angiosperms, insects
  3. Paraphyletic Group
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    • Consists of ancestral species & some, but not all, of the common descendants
    • ex. dinosauria, fish, gymnosperms
  4. Polyphyletic Group
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    • Consists of various species that lack a common ancestor
    • ex. marine mammals, bipedal mammals, flying vertibrates, trees, etc.
  5. 1. Why we can't build a phylogenetic tree on traits alone:

    2. Which tree is correct?

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    1.Similarity doesn't always indicate recent shared ancestry! (polyphyletic, ex. traits can appear separately)

    • 2. Bats & dogs are sister taxa. So sometimes closer relation looks different too!
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  6. How to build a phylogeny? =How do we infer evolutionaryrelationships?
    • Measure as many heritable characters/traitsas possible in the group of organisms
    • External and internal morphology (skeleton),behavior, cell structure, chromosome #,nucleotide sequences in DNA, etc.More shared traits = more closely related
  7. Homology (definition)
    Character state shared b/w 2+ species b/c it was present in common ancestor

    (USE THIS to make phylogeny)

    • ex. mammals lactate b/c 1st made milk
    • ex. homologous bones

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  8. Homoplasy (definition)
    • Trait shared b/w 2+ species that was NOT present in a common ancestor
    • ex. Placental mole is closer to a human than a Marsupial mole. They went through convergent evolution from environment to look similar

    (DONT USE to create phylogeny!)
  9. Convergent Evolution
    • Unlrelated but similar features. Happens to organisms living in similar environments.
    • See in polyphyletic groups
    • ex. moles; marsupial mole closer to kangaroo, placental mole closer to humans
  10. How many times does:
    homology evolve?
    homoplasy evolve?
    • - ONLY ONCE

    *So homology more common b/c not so likely to happen more (like winning lottery), very low odds to hit it more than once!
  11. Parsimony
    • The simplest explanation is the most correct
    • In terms of a phylogeny, the likely correct one is the MOST SIMPLEST ONE

    • ex. Tree: 2 changes of gaining trait vs Tree: 6 changes of losing trait -> 2 changes WINS
    • ex. 30 genes. 27 same -> Homology
    • 3 different -> Homoplasy
  12. Synapomorphy
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    Derived trait, evolved after a common ancestor & shared
  13. Homologies = Ancestral vs Derived
    Which of these is most helpful?
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    • Derived more useful.
    • a = ancestral
    • a' = derived

    C is most helpful b/c the outgroup is a (ancestral)
  14. Steps to building a phylogeny:
    • 1. Choose your organism.
    • 2. Identify heritable characters that showvariation among organisms
    • 3. Identify the versions of each characters for allorganisms
    • 4. For each pair of organisms, calculate thenumber of differences.
    • 5. Create the most parsimonious tree.
  15. 7 Requirements of Life:
    • 1. Order = 2nd law of thermodynamics: Entropy - Increasing order takes work/energy
    • 2. Regulation = Homeostasis
    • 3. Growth & development = Basic cell theory: All living things have 1 or more cells, all cells come from other cells
    • 4. Energy utilization
    • 5. Response to environment = Jumping out of way of car?
    • 6. Reproduction = Sexual/asexual, meiosis/mitosis
    • 7. Evolution

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  16. 4 Steps that hypothesize how life began:
    • 1. Synthesis of organic molecules
    • ex. Miller-Urey experiment, UCSD, recreated early atmosphere & got spontaneous formation of amino acids...building blocks of life. (Likely they appeared near ocean volcanoes & deep sea vents).
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    • 2. Synthesis of polymers: Large molecules made from smaller ones. Form into proteins, carbs, lipids, nucleic acids-> consist of RNA/DNA.
    • Enzymes=300-400 amino acids strung together. Small organic molecules polymerize when they're concentrated on hot sand, clay, rock
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    • 3. Protobionts (Pre-cells)
    • Collections of organic molecules in membranes. Simple reprooduction, metabolism, homeostasis.
    • Phospholipid membrane. Packaging.
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    • 4. RNA: First genetic material.
    • It can self replica, splice; mRNA, tRNA, rRNA; many functions. More versatile, less stable. Early portobionts w/ self-replicating RNA; because of heritable genetic material, capable of mutation, variation, & increase through natural selection.
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  17. PRECAMBRIAN & 6 Evolutionary Milestones
    • 4.6 BYA - 540 MYA
    • 1. LIFE ARISES (building blocks) = Primordial ooze. Early earth molten, capacity for life early.
    • 2. Cells form = Prokaryotic cell.
    • 3. Photosynthesis = Cyanobacteria (blue-green), Byproduct of photosynthesis -> Oxygen increases -> Important for aerobic cells & organism. Large population growth
    • 4. Sex = Bacterial conjugation.
    • Sex pilus, exchanges genetic info. Horizontal gene transfer that creates drug resistance, exchanges DNA
    • 5. Eukaryotes ~2.1 BYA
    • Endosymbiotic Theory = Several key organelles of eukaryotes originated as symbioses between separate single-celled organisms
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    • 6. Multicellularity = Volvox: Multicellular protist
    • Differentiation = Cells have own functions
    • Colonial = Group of cells, same function
  18. Homeotic Genes (definition)
    • Early determination of where your parts are located.
    • ex. fruit fly w/legs on face, just by changing one gene "instruction"
    • 540 MYA
    • Beginning of Paleozoic period
    • Not really an explosion, but a bloom of diversity
    • Small changes in control genes led to large changes in bodies
    • ORIGIN of modern body plans
    • Evolution was BUILDING TO THIS POINT
    • In less than 100,000 yrs, MOST MODERN PHYLA CAME TO BE

    • WHY???
    • 1. Fossil record incomplete, diversification could have begun earlier
    • 2. Tens of millions of yrs still very long time for evolution to take place
    • 3. Key innovations such as jointed appendages & jaws may have lead to rapid co-evolution. Motile jawed predators select for defenses of prey (leads to snowball effect of evolution)
  20. PALEOZOIC Period
    "Ancient Era"
    • 540 MYA to 250 MYA
    • Pangaea
    • 96% all species extinct due to massive volcanic eruption & CO2 & SO2 (methane) caused global warming positive feedback loop. Massive release of methane altered global ocean circulation, causing oceans to be anoxic (lacking oxygen) where most life was
  21. Background vs Mass Extinction
    Background extinction = Natural process. Most.

    Mass extinction = Large percentage extinct in short period of time (global event, broad range of organisms, rapid relative to expected lifespan of taxa). Global diversity disappears, then quickly gain diversity from survivors b/c they have new chance to evolve, become dominant, etc.

    5 major mass events, we are now in our 6th = HUMAN-CAUSED
    "Middle Era"
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    • 250 MYA - 65 MYA
    • "Age of the Dinosaurs"

    • Pangaea in process of dividing
    • Walter Alvarez (UC Berkeley) discovered worldwide iridium layer in ash (commonly found in meteorites in SPACE)...

    • Chicxulub Crater at the K/T Boundary 65 MYA (Cretatious/Tertiary boundary)
    • At this time continents separate
    • Dinosaurs didn't go totally extinct (BIRDS & REPTILES ARE DINOSAURS)
    • Mammals did not originate...Lived at the time but were small, shrew-like. After dinosaurs, main predators gone, mammals became dominant predator
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    "Recent Era"
    • 65 MYA - Present
    • "Age of Mammals"...but also age of:
    • INSECTS, floewring plants, fish, birds
  24. Adaptive Ratiation
    • When organisms diversify rapidly into a multitude of new forms, particularly when a change in the environment makes new resources available and opens environmental niches.
    • ex. hawaiian islands & Tarweed relatives
    • a
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    • Eukarya
    • Archaea
    • Bacteria

    • (largest branches on tree of life)
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  27. Virtually all members of the bacteria & archaea are ____________ and all are _____________
    • Unicellular
    • Prokaryotic
    "Before Kernel"

    (4 Main features & other facts:)
    • 1. Lots of shapes
    • 2. No membrane-bound organelles
    • (NO NUCLEUS)
    • 3. Unicellular
    • 4. Cell wall

    • Include Domains: Bacteria & Archaea
    • Extremophiles = Can live EVERYWHERE (too acidic, too salty, too cold, too hot)
    • The # of Prokaryotes in a handful of soil are greater than  the # of people who have ever lived!
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  29. Lateral Gene Transfer (definition)
    • Evolved once, moved to species in another lineage
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    • Main cause of antibacterial resistance
    • Significant in Prokaryotes or unicellular Eukaryotes

    (In relation to Eukarya)
    • NO DNA enclosed in nuclear envelope
    • NO nucleus
    • NOT multicellular (except some bacteria)

    • Circular chromosome
    • Rotating flagella
  31. Are there more eukaryotic cells in the human body or bacterial cells?
    Bacterial - There's 10 TIMES more bacterial cells in the human body than eukaryotic!
  32. Morphological Diversity
    (dealing with form & structure)
    3 ways bacteria & archaea most diverse:
    • 1. Size. From .3 micrometer to 100
    • 2. Shape. From rods, speres, spirals, chains
    • 3. Motility. Some don't move, some swim, some flagella movement, some glide
  33. Cell-Wall Composition
    (& Gram Stain)
    • In BACTERIA, 2 general types of cell walls
    • Gram stains PEPTIDOGLYCAN (a polymer). If dark/purple=more (gram+). If light/pink= less (gram -).

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  34. The most distinct and important thing about bacteria & archaea is how diverse they are in: _____________________________________
    The types of compounds they can use as food.
  35. In regards to metabolism, all organisms must obtain:

    • 1. Chemical energy as ATP
    • 2. Carbon compounds that can serve as building blocks for synthesis of cellular components
  36. Bacteria & archaea may use 1 of 3 sources of energy for ATP production:
    • 1. Light:
    • (by Phototrophs. Produce ATP by photophsosphorylation. Water donates electrons)

    • 2. Organic molecules:
    • (by Chemoorganotrophs. Oxidize organic molecules w/ potential energy. Oxidized by snapping chemical bonds, releasing energy. Cellular respiration or fermentation. Sugars donate electrons).

    • 3. Inorganic molecules:
    • (by Chemolithotrophs. Oxidize inorganic molecules w/ potential energy. Cellular respiration. Inorganic compounds donate electrons)
  37. How bacteria & archaea obtain building-block compounds:
    = 2 groups (6 subgroups)
    *Bacteria/Archaea use all 6*

    • Autotrophs "Self-Feeding" = Synthesize them from simple starting materials (Carbon source CO2)
    • - Photoautotrophs from light source
    • ex. Photosynthetic protists; PLANTS, algae, cyanobacteria
    • - Chemo(litho)autotrophs from inorganic chemicals/molecules
    • - Chemo(organo)autotrophs from organic compounds/molecules

    • Heterotrophs = Absorb them from their environment (Carbon source organic compounds)
    • - Photoheterotrophs from light
    • - Chemo(organo)heterotrophs from organic compounds/molecules
    • ex. protists, fungi, animals, some plants
    • - Chemo(lithotriphic) heterotrophs from inorganic chemicals/molecules
  38. Disease-Causing Archaean
    1st discovered in 2004 - Dental Periodontitis
  39. Disease-Causing Bacteria
    • Known as Pathogenic (only small amount)
    • Tend to affect tissues at entry points
  40. Disease-Causing Bacteria:
    Lineage (Order): Firmicutes

    Mneumonic: "Be FIRM on clean locker rooms"

    • Steptococcus pneumonia - Pneumonia
    • Streptococcus pyogenes - Strep throat
    • Staphylococcus aureus - MRSA (Methicillin-resistant Staphylococcus aureus)
  41. Disease-Causing Bacteria:
    Lineage (Order): Spirochaetes

    Mneumonic: Spiral worms like ticks.

    • Borrelia burgdorferi - Lyme disease
    • Treponema pallidum - Syphilis
  42. Disease-Causing Bacteria:
    Lineage (Order): Actinobacteria

    Mneumonic: ac->acne t ->tb

    • Mycobacterium tuberculosis - Tuberculosis
    • Mycobacterium leprae - Leprosy
    • Propionibacterium - Acnes
  43. Antibiotics don't treat against __________, only ______________.
    • Virus
    • Bacteria
  44. Clostridium
    Bacterial infection. Can disrupt all the bacteria in our gut, ridding it of the bacteria we need.

    Solution: Human probiotic infusion= "POOP TRANSPLANT"
    (Main features, classification, facts)
    • Characterized by:
    • 1. Nucleus & Nuclear envelope
    • 2. Asexual & sexual reproduction
    • 3. Organelles
    • (Multicellularity is common)

    • Cells are 10X LARGER than archaea or bacteria & they are COMPARTMENTALIZED= Distinct functions.
    • Range from: Single-celled; size of bacteria, to sequoia trees & blue whales (largest)
    • 3rd DOMAIN on tree of iife
  46. Protists (Facts & Characteristics)
    • "Catch All" Group
    • All Eukaryotes that are NOT green plants, fungi, animals
    • 10% of Eukarotes

    • Characteristics:
    • 1. Live in aquatic/moist areas
    • 2. Include all 5 lineages of Eukarya,
    • (except 2 taxa)
    • 3. Internal support: SILICON SKELETON
    • 4. External support: TEST/SHELL
    • 5. Feedi by way of: Ingestion, absorption, photosythesis
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  47. There are ____ Major lineages of Eukarya, all include _________, 2 include taxa that aren't.
    • 5
    • protists
  48. 3 Feeding strategies of Protists:
    • 1. Ingestion:
    • - Pseudopodia ("fake feet")
    • - Filter feeders

    • 2. Absorption: 
    • - Decomposer (feeds on dead organic matter)
    • - Parasite: Lives on or on a host, damaging it

    • 3. Photosynthesis
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  49. Eukaryote Supergroups:


    Mneumonic: " EXCuse me while I diahhrea & sleep"
    • Modified mitochondria 
    • ex. Giardia

    • Sprial rod in Flagella
    • ex. Trypanosomiasis: African sleeping sickness. Swelling of brain. Recognized by flagella

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  50. Eukaryote Supergroups:


    Mneumonic: Chrome=red (red tide)
    • Dinoflagellates - membrane bound sacs beneath plasma membrane
    • ex. RED TIDE

    • Golden algae, Brown algae - harry & smooth flagella
    • ex. Brown alagae = SEA KELP

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  51. Brown Algae
    • All are multicellular, most marine
    • Include "Seaweeds" & giant = Kelp
    • Bull-kelp, featherboa, provide food for kelp forest & entire ECO SYSTEM THRIVES ON IT
    • Kelp lives in deep parts of ocean
    • Algal body is plantlike but no roots :

    • - Thallus is entire algal body
    • - Holdfast like roots/anchor
    • - Stipe = like stem
    • - Blade = like leaves
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  52. Eukaryote Supergroups:


    Mneumonic: "RISE from their shell fossils"
    Foraminifera = Tiny, shells, many of fossil records. Marine protists. Very diverse. Have appendages. Mostly unicellular

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  53. Eukaryote Supergroups:


    Mneumonic: Many of my PLANTS are PLASTIC
    Major Clades:

    • 1. Red algae - Sushi paper
    • 2. Green algae - Toxic sea lettuce (Can have huge blooms from influx of nutrients. When dead, creates noxious gas - In France killed 13 people when cleaning it up!) Green from chloroplasts/chlorophyl.
    • 3. Land plants - NON-PROTISTS! mosses, ferns, conifers, flowering plants
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  54. Eukaryote Supergroups:


    • Amoebas - Slime molds
    • ex. Peapoly cephyllum (slime mold): Single-celled organism. In lab, can do maze in optimal route, leaves chemical trail so knows what space it explored, when different foods, goes to best one. Not smart INDIVIDUALLY, but Self-Organized. Thrive in groups.

    • Choanoflagellates & other 2 NON-PROTISTS!
    • = animals, fungi
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  55. Miller-Urey-type experiments have shown that

    A) living cells could survive in primitive Earth's atmosphere.
    B) microspheres could be formed from amino acids.
    C) simple cells could be produced in the laboratory using a "soup" of small organic molecules.
    D) given the conditions of early Earth, the formation of life would still require additional materials from meteorites and asteroids.
    E) complex organic molecules can be produced by physical processes from inorganic components.
    E) complex organic molecules can be produced by physical processes from inorganic components.
    (this multiple choice question has been scrambled)
  56. A current leading hypothesis about the first system of inheritance in the earliest life forms involves

    A) lipids that directed the synthesis of simple proteins.
    B) self-replicating polypeptides aided by ribosomes.
    C) self-replicating RNA molecules aided by ribozymes.
    D) proteins that served as templates for RNA molecules, leading to the formation of DNA.
    E) self-replicating DNA molecules (the "DNA world" hypothesis).
    C) self-replicating RNA molecules aided by ribozymes.
    (this multiple choice question has been scrambled)
  57. During the __________, over 96% of marine species and many terrestrialspecies became extinct, possibly because intense volcanic activity warmed Earth's climate.

    A) Cenozoic
    B) Mesozoic
    C) Permian
    D) Precambrian
    E) Cretaceous
    C) Permian
    (this multiple choice question has been scrambled)
  58. Which of the following organisms first introduced oxygen into Earth's atmosphere?

    A) early protozoans
    B) cyanobacteria
    C) methanogens
    D) green algae
    E) plants
    B) cyanobacteria
    (this multiple choice question has been scrambled)
  59. 33. (3 pts) Chemoautotrophic bacteria obtain their carbon from _____ and their energy from _____ .

    A) methane . . . sunlight
    B) CO2 . . . reactions involving inorganic chemicals
    C) organic molecules . . . enzymes
    D) CO2 . . . sunlight
    E) organic molecules . . . sunlight
    B) CO2 . . . reactions involving inorganic chemicals
    (this multiple choice question has been scrambled)
Card Set
BILD 3 Midterm 2: Speciation & Origin of Life
BILD 3 UCSD organismic evolutionary biology
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