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BIOL213 Chp25~35

Y N Biology Englisch

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BIOL213 Chp25~35

BIOL213 Chp25
- What is fossil
  - strengths
    - used for studying the history of life
      - PHYLOGENETIC TREE
        What is Phylogenetic tree?
        Simplified diagram
        describing organisms evolutionaly histories
        studied by fossil records
        powerful tool for studying the history of life
        Why??
        convenient to see the relationship between species
        as well as evolutionary histories
        TYPES OF GROUPING ( EVOLUTIONARY UNITS)
        This is divided by traits
        (1) Monophyletic Group (clade)
        Divided by Synapomorphy of organisms
        (2) Polyphyletic Group
        Sharing similar traits
        They developed independently
        (3) Paraphyletic Group
        Having the same traits in one large group, but not all species
        COMPLICATION IN GROUPING
        Homology v.s. Homoplasy
        Homology
        Organisms are similar due to common ancestory
        Homoplasy
        Organisms having similar traits which they evolved independently
        Homologous v.s. Convergent (Both are Homoplasy)
        Homologous
        Having common ancestors at some point
        Convergent
        Organisms living in similar environment
        How to group organisms??
        Show evolutionary related ness
        Study organisms
        Making data set
        There are so many possibilities
        How to make a data?
        Filtering methods
        (1) Parsimony
        Data with less evolutionary changes are more likely
        (2) Evolutionary distance
        More rapid evolutionally changes are more likely
        (3) Maximum likelihood and Bayesian analysis
        Research DNA sequences
        Formation
        Root
        the most ancestral branch
        Node
        the most recent common ancestor
        show where do they split
        Outgroup
        groups that don't have the same traits
        Sistergroup
        species or groups that are closely related
        Branch
        line representing the relatedness
        Branch Lengths
        (1) Show how species diverged
        (2) Show when species extinct
        Tip
        each specie
        MISUNDERSTOOD!!
        (1) the nearest branch does not represent the closest specie
        amount of nodes do not represent how many revolutions ocuured
        trees can be drawn differently
        Traits
        Characteristics of species
        TYPES OF TRAITS
        Synapomorphy
        traits that found in two or more groups
        present in most recent common ancestor
        Apomorphy
        traits that developed individually
        CLADISTIC APPROACH
        grouping method of species
        based on phylogenetic trees
        Clades
        Groups of species = clades
        Lineages
    - evolutionary history
  - Weaknesses
    - Fossil biases
      - Habitat Bias
        Organisms living in specific environment = more likely to fossilize
      - Toxanomic & Tissue Bias
        Organisms with hard body parts = more likely to fossilize
      - Temporal Bias
        Organisms born recently = their fossils likely to be found
      - Abundance Bias
        Organisms with larger population = their fossils likely to be found
  - In what environment do they form
    - (1) when they buried rapidly
    - (2) when they decompose slowly
  - piece of physical evidence
  - from organisms lived in the past
  - FOSSIL RECORDS
    - Types of Fossils
      - Intact fossil
        Organisms remain undamaged
      - Compression fossil
        sediment compress organisms
      - Cast fossil
        organisms decomposes
        leaving just shapes of organisms
      - Perminerized fossil
        organisms decompose slowly
        minerals turn organisms into stone
      - Trace Fossil
        Organisms' footprint and tracks remain
    - Used to estimate The Life's Time Line
      - LIFE'S TIME LINE
        Hadean Eon
        Archaean Eon
        Proterozoic Eon
        Phanerozoic Eon
        Paleozoic era
        Mesozoic era
        Cenozoic era
        First cynobacteria
        First eukaryotic cells
        First Photosynthetic Eukaryotic cells
        First multicellular organisms
        First oceans
        Origin of life
        Photosynthetic cells
        First oxygen formation
        Earth formation
        Major evolutionary events
        Cambrian Explosion: Diversification of animals
        First arthropods, mollusks, vertebrates
        Land plants
        Bony fish, tetrapods, plants with seeds
        origin of amniotes
        First dinosaurs, mammals
        Bird like reptile, angiosperm, bee, ant
        First horses, rabbits
        fully aquatic whales
        chimpanzees
        Adaptive Radiation
        Single lineage rapidly produce many species
        Cambrian explosion
        Why does this occur??
        Ecological opportunity
        More resources
        Few competitions
        Innovations
        Morphological
        Formation of reproductive structure that helped diversifying
        Physiological
        Ability to live in new environments, ability to fly
        Behavioral
        Birds started dancing when they attract others to find mates
        Environmental change
        Mutation favored by natual selection
        Dominant Taxa
        Diverse of animals, land plants, fungi
        Plants: Gymnosperms Animals: Dinosaurs
        Plants: Angiosperms Animals: Birds & Mammals
        Mass extinction
        Ordovician Extinction
        Devonian Extinction
        Permian extinction
        Triassic Extinction
        Cretaceous Extinction
        Asteroid impact
        the largest tsunami
        blocked the Sun for long periods
        extensive acid rain
        Caused by Flood basalts (volcanos)
        acid rain > devastated plants and organisms
        oceans lacked oxygen > sealevel dropped
        Extinctions
        Background extinction
        lower, natural, and average rate of extinction
        normal environment change
        competition to other species
        rapid extinction of large number of diverse species
        Occur in extraordinary and sudden change in environment
        4570 mya
        4000 mya
        3700 mya
        3600 mya
        3000 mya
        2500 mya
        541 mya
        485
        444
        359
        299
        252
        201
        66
        Present
        145
        1000 mya
BIOL213 Chp27
- Eukaryotes
  - Eukarya
    - Characters
      - larger cells
      - More organels
      - more extensive cytoskelton
      - Having nuclear envelope
      - evolving multicellularity
      - reproduce asexually and sexually
    - Evolution
      - Evolved to...
        Protists
        What are protists?
        Paraphyletic group
        very diverse
        most are unicellular
        some are multicellular
        or form aggregations called colonies.
        Important to
        Human
        Diseases (Malaria etc) are caused by protists
        Ecology
        Photosynthetic protists
        Fix CO2
        Forming sugers
        other organic compounds
        They are primary producers
        Base of the aquatic food chain
        Plankton
        Understanding evolution of other organisms
        How to discover new lineages?
        Direct Sequencing
        Steps
        (1) based on sampling soil or water
        (2) analyzing the DNA sequence of specific genes
        (3) using the data to place the sample on a phylogenetic tree
        PROTISTS KEY INNOVATIONS
        (1) mitochondria
        Endosymbiosis Theory
        What is mitochondria
        organels
        generate ATP
        use pyruvate as an electron donor
        oxygen as the ultimate electron acceptor
        (1) a bacterial cell took up residence inside another cell
        Evidence
        Mitochondria have their own genomes, which are organized as circular molecules—much like a bacterial chromosome
        > Host cell provides
        protection
        O2
        > Bacteria provides
        ATP
        (2) The bacterial cells are transmitted to offspring in eggs or sperm
        (2) Chloroplasts
        (3) nucleus and endomembrane system (nuclear envelope)
        Infoldings of the plasma membrane
        (1) rise to small infoldings
        (2) elaborated by mutation and natural selection over time
        (3) left (detached) from the plasma membrane
        Evidence
        Infoldings of the plasma membrane occur in some bacteria
        nuclear envelope and ER of today’s eukaryotes
        Advantage
        Transcription and translation
        RNA transcription: Inside
        translation :outside the nucleus
        simple nuclear envelope > many ways to do RNA
        Transcription
        making RNA copies of genes
        from DNA
        Translation
        converts RNA > into protein
        better way to control gene expression!!
        (4) Support structure (Cell walls)
        (5) Multicellularity
        (6) cytoskeleton
        Lead by mutations
        (1) cells simply stick together after cell division
        (2) Natural selection favored
        (3) cells became larger and specialized for different functions
        specialized for producing or obtaining food
        specialized for reproduction
        Advantages
        cells communication
        finding food
        moving
        reproducing
        Types of cell walls
        (1) cell walls outside their plasma membrane
        cell wall of silicon dioxide
        Diatoms
        Used for surviving from prayers
        After the extinction, they evolved from volcanic dust
        cell wall of cellulose plates
        Dinoflagellates
        (2) hard external structure (shell)
        chambered calcium carbonate shell
        Rhizaria
        (3) rigid structures inside the plasma membrane
        collection of protein strips
        Excavata
        Name of structure
        Name of organisms
        How they evolved these
        what is nuclear envelope
        The double-layered membrane
        enclosing the nucleus of a eukaryotic cell
        what is ER (endoplasmic reticulum)
        network of membranes
        making lipids and proteins
        (1) photosystems I and II evolved in bacteria
        (2) photosynthetic bacterium provided its eukaryotic host with
        oxygen
        glucose
        Evidence
        Chloroplasts contain a circular DNA molecule containing genes that are extremely similar to genes found in various species of cyanobacteria.
        (3) the host provided the bacterium
        protection
        access to light
        Endosymbiosis Theory
        In Excavata, Rhizaria, Alveolata, and Stramenopila
        In Plantae lineage
        Plantae Lineage
        CH
        Green algae
        What's Green Algae?
        photosynthetic organisms
        aquatic habitats
        OCEANS
        Green Algae that are the most similar to land plants
        Zygnematophyceae
        Coleochaetophyceae
        Charophyceae
        ↑Closest living to land plants
        They are...
        Multicellular
        Living in fresh water
        = LAND PLANTS evolved from freshwater green algae!!
        Land Plants
        What are land plants?
        key photosynthesizers
        terrestrial environments
        LAND
        Befenits
        (1) Provide Ecosystem Services
        Produce O2
        Build and hold soil & water
        moderate climate
        being a primary producers
        (2) Humans
        Food
        Fuel
        Fiber and Building Materials
        Medicines
        How Land plants evolved?
        We search for...
        (1) morphological traits
        (2) the fossil record
        (3) phylogenetic trees (DNA sequence)
        The phylogeny
        Plantae
        Green plants
        Green Algae
        Nonvascular plants (bryophytes)
        Seedless vascular plants
        Gymnosperms
        Angiosperms
        Outgroup of Gymnosperms
        Flowers, fruits
        ANGIOSPERMS
        Reproduction cycle
        Male part (Anther)
        (1) Meiosis: Sporophyte produce pollen grain (male gametophyte)
        (2) Mitosis: pollen multiply
        Female part (Ovary)
        (1) Meiosis: female gamete is made
        (2) female gamete is multiplied
        (3) Double fertilization: male come into female
        (4) Mitosis: Fruits develops
        (5) Mitosis: Sporophyte develops
        Monophyletic
        GYMNOSPERMS
        Reproduction cycle
        Male cone
        (1) Meiosis: Male cone produce pollen (male gametophyte)
        (2) Mitosis: Pollen divide
        Female cone
        (1) Meiosis: mother cell produce daughter cell
        (3) Fertilization: Pollen go into daughter cell > become zygote (2n)
        (4) Seeds are spread
        (5) They become sporophyte (the trees)
        Paraphyletic
        Vascular tissue
        Seed plants
        Monophyletic
        Seeds
        SEED PLANTS
        SEEDLESS VASCULAR PLANTS
        Reproduction cycle
        (1) Meiosis: Sporopyte produce spores
        (2) Mitosis: Mature gametophytes
        (3) Mature gametophytes produce eggs and sperm
        (4) Fertilization: Zygote (2n) is made
        (5) Mitosis: Zygote become sporophyte
        Paraphyletic
        Ability to live on land
        Land's resources
        Light
        Carbon Dioxide
        NON VASCULAR PLANTS
        Reproduction cycle
        (1)Meiosis: Sporophyte (2n) produces spores
        (2) Mitosis: spores grow taller > become male/female gametophytes
        (3) Fertilization: Zygote (2n) born
        (4) Mitosis: Mature gametophyte & Sporophyte
        Paraphyletic
        Some evolved photosynthetic structure
        Land plants
        Monophyletic
        GREEN ALGAE
        Monophyletic
        Grouping
        Traits evolved
        Evolutions
        HOW THEY PREVENT FROM DRYING OUT?
        (1) preventing water loss
        Cuticle (waxy sufface prevent water evapolation)
        Stomata (allow CO2 into the leaves for photosynthesizing)
        (2) providing protection from UV
        flavonoids
        function as a sunscreen
        (3) moving water from tissues
        (1) water-conducting tissue
        water could move from the base of the plants upward
        (2) Lignin developped (made plants strong)
        (3) Tracheids & secondary cell wall evolved
        HOW THEY REPRODUCE?
        Dominant phase in life cycle
        Gametophyte (n) Dominant
        Sporophyte (2n) Dominant
        Sporophyte (2n) Dominant
        HOW THEY PRODUCE GAMETES
        homospory
        heterospory
        produce two distinct types of spores
        different structures
        (1) Microsporangia: become male gametophyte
        (2) Megasporangia: become female gametophyte
        production of a single type of spore
        ALTERNATION OF GENERATIONS
        No alternation
        Reproduction cycles
        TYPES OF GREEN PLANTS
        Time Periods
        Origin of Land Plants
        Silurian–Devonian Explosion
        The Carboniferous Period
        Diversification of Gymnosperms
        Diversification of Angiosperms
        First flowering plants
        both flowers and fruits
        ADAPTIVE RADIATION
        Why?
        3 key adaptations
        (1) water-conducting vessels
        (2) flowers
        (3) fruits
        Several types of angiosperms
        (1) Monocots
        (2) Eudicots
        (3) Neither monocots not eudicots
        (4) Others (original)
        First plants with seeds and pollen
        in wet and dry environments
        land covered by green plants
        Extensive coal-forming
        club mosses, horsetails abundant
        Most major morphological innovations
        Stomata, vascular tissue, roots, leaves
        First evidence
        Spores, sporangia, cuticles are found
        Events
        mya
        475
        416
        359
        299
        145
        1. Similarities
        (1) chloroplasts contain the photosynthetic pigments
        (2) have similar arrangements of membrane-bound sacs
        (3) cell walls, sperm, and peroxisomes are similar in structure and composition
        (4) chloroplasts synthesize starch
        2. Differences in Land Plants
        (1) Nonvascular plants (bryophytes)
        lack vascular tissue
        Lack seeds
        (2) Seedless vascular plants
        Lack seeds
        (3) Seed plants
        have vascular tissue
        have seeds
        Types of seed plants
        Gymnosperms
        Angiosperms
        flowering plants
        Evolved first
        Types of plants
        Plant Form & Function
        Shoot
        Structure
        Diversity of Shoot structure
        (1) Morphological Diversity
        (2) Phenotypic Plasticity
        (3) Modified Shoot
        (1) Water-storage structures
        (2) Stolons
        (3) Rhizomes
        (4) Tubers
        (5) Thorns
        provide protection
        Store carbohydrates (starch)
        grow horizontally under the soil
        produce nodes along the soil surface
        Stores water in dry environment
        The shape and size vary based on
        temperature, wind, water, nutrients, and light
        If plants are in shaded region
        (1) Plants grow toward to light
        (2) Producing more leaves and roots
        They have different size and structure to avoid competition
        to also survive in different environemt
        (1) Lush habitats
        competition for light is intense
        taller plants are favored
        (2) Dry habitats
        short stem plants are favored
        they don't require much water
        Function
        Absorbing light
        transport sugar to root
        Through vascular tissues
        Transport sugar to shoot
        Root
        Structure
        Diversity of Root structure
        (1) Morphological Diversity
        (2) Phenotypic Plasticity
        (3) Modified Roots
        Roots become advantageous
        depending on the environement
        (1) Anchor roots
        (2) Prop roots
        (3) Pneumatophores
        (4) Storage roots
        store sugar
        function in gas exchange
        protect them in windy weather
        stick on the walls
        their form can change
        depending on environment
        (1) Roots growing
        into areas with abundant resources
        (2) Stop growing
        areas where resources are used up
        They vary in lengths to avoid competition
        (1) fibrous root systems
        (2) taproot systems
        one long & thick root
        no taproot (long & tough root)
        short & many thin roots
        Function
        Absorb nutrients and water from soil
        send these to shoot system
        Leaves
        Structure
        Diversity of Leaf structure
        (1) Morphological Diversity
        (2) Phenotypic Plasticity
        (3) Modified Leaves
        some leaves perform other roles
        (1) Onion bulbs
        store food
        (2) Aloe Succulent leaves
        store water
        (3) Tendrils
        help climbing
        (4) Floral mimics (red leaves)
        attract insects
        (5) Traps
        Trap insects and digest them
        depending on whether if the leaves are on sun or shade
        (1) Sun leaves
        Thicker
        small SA
        Reduce water loss
        (2) Shade leaves
        Thin
        high SA
        Maximize absorption of sunlight
        A. Shapes/Sizes of leaves
        Simple leaf
        Compound leaf
        Doubly compound leaf
        Needlelike leaves
        Deserts or cold area
        B. Arrangement of leaves
        Alternate leaves
        Opposite leaves
        Whorled leaves
        Rosette
        Their shape/size differ depending on environment
        Function
        Part of shoot system
        Place of photosynthesis
        SA to Volume Ratios
        Surface
        Absorption
        associated with...
        root & shoot
        Volume
        associated with...
        cells that use molecules and lights
        Large SA to V ratio
        more efficient in absorption
        leaves & shoot & root
        Low SA to V ratio
        not associated with absorption
        tubers & seeds
        What is a plant?
        Intermediate growth
        plants continue to increase
        overall body size
        show plasticity
        changes their
        morphology
        behavior
        physiology
        in response to the environment
        Basic Form
        Tissues
        Primary Growth
        Water Transport
        Sugar Transport
        Primary Growth
        Apical meristems
        Meristematic Growth
        Secondary Growth
        what is meristems?
        populations of undifferentiated cells
        they undergo mitosis
        Lateral meristems
        responsible for primary growth
        Types of meristems
        (1) Protoderm
        (2) Ground meristem
        give rise to...
        location
        what is primary growth?
        increase in the length of stems and roots
        make primary plant body
        Primary Root System
        Primary Shoot System
        Tissues
        Dermal Tissue System
        Ground Tissue System
        Vascular Tissue System
        Xylem
        water conductiin cells
        tracheids
        present in all plants
        vessel elements
        present in angiosperms and other vascular plants
        they are found together in vascular plans
        dead at maturity
        contain no cytoplasm
        Transport of water and nutrients (from ROOT to SHOOT)
        structural support
        fibers
        from root to shoot
        Phloem
        sieve-tube elements
        long, thin cells
        transporting sugars, amino acids, hormones, etc. and other nutrients
        structural support
        few organelles
        companion cells
        many organelles
        attached to companion cells
        provide materials for sieve-tube elements
        structural support
        frequently fibers
        dead at maturity
        from root to shoot
        COMPLEX TISSUES
        Parenchyma
        contain chroloplasts (leaves)
        contain starch storage (root)
        only promaly cell walls
        Photosynthesis
        Sugar and other compounds storage
        found in leaves & roots: potato & apples are made by this
        Collenchyma
        longer and thinner
        unevenly thickened
        Flexible cell walls
        flexible structural support in stems
        support actively growing part
        support actively growing part
        found in stem of celery
        Sclerenchyma
        sclereids
        variable shapes
        short
        Protection
        (hard outer surface of seeds and fruits)
        found in pears
        fibers
        very long
        support (stems and leaves)
        found in stems & leaves
        Primary (cellulose) and secondary (c. +lignin) cell walls
        dead at maturity
        SIMPLE TISSUES
        Epidermis
        flatted
        Protect the surface
        regulate gas exchange and water loss
        water and nutrient absorption
        produce waxy cuticle (leaves)
        lack chloroplasts
        Stomata (leaves)
        surrounded by two guard cells
        regulate gas exchange and water loss
        regulate water loss
        Trichomes
        hairlike
        (1) keep the leaf surface cool
        (2) reduce water loss
        (3) provide barbs or store toxic compounds
        COMPLEX TISSUES
        These are found behind the leaves
        Tissue present
        Function in root
        Function in Shoot
        structure
        Structure
        Function in shoot
        Function in shoot
        where are these found
        where are these found
        Basic Form
        LAND PLANTS EVOLVED FROM GREEN ALGAE!
        Evolution of OCEANS > LANDS
        Evidence
        (1) key traits are similar in the two groups
        (2) green algae appear long before land plants based on fossil record
        (3) DNA sequence data
        Secondary Endosymbiosis Theory
        They have four membranes
        (1) They first engulfs chloroplast
        (2) the organisms with chloroplast is eaten by other protists
        How they evolved these??
        How do ptotists...
        (1) Eat
        (2) Move
        (3) Reproduce
        (1) Asexual reproduction
        mitotic cell division
        What is mitosis
        nuclear division
        results in two daughter nuclei
        (2) Sexual reproduction
        meiotic cell division and fusion of gametes
        What is meiosis
        one diploid (2n) parent cell > produces haploid (n) cells (gametes)
        2n
        n
        Why evolved??
        genetically variable offspring = better chance of surviving
        if the environment changes
        an adaptation to fight disease
        Life Cycles of Protists
        sequence of events
        grow > mature > reproduce
        Evolution
        Meiosis
        Haploid (n) and diploid (2n) phase
        single-celled protists
        (1) Types of reproduction
        Asexual reproduction
        Mitosis >growth
        (1) Haploid (n) most of the time
        (2) Diploid most of the time
        or Asexual + Sexual
        Sexual reproduction
        Meiosis (changes 2n to n) >Fertilization (changes n to 2n) > growth
        (1) Haploid (n) most of the time
        (2) Diploid most of the time
        (2) gametes are the only haploid cells
        (1) meiosis occurs in the mitotically produced offspring
        or Sexual + Asexual
        How it grows
        Dominants
        Multicellular protists and Land Plants
        alternation of generations
        Repeating both Haploid and Diploid phases
        Phase
        Step
        SPOROPHYTE
        (1) Diploid generation (2n)
        (1) produce different sex of spores (n)
        by meiosis
        GAMETOPHYTE
        (2) Different sex of spores (n)
        (2) produce gametes (n)
        by mitosis
        multicellular haploid form (n)
        FERTILIZATION
        both gender of gametes meet
        (3) Different sex of gametes fertilize
        (3) form zygote (2n)
        MATURATION
        become taller
        Zygote (2n) become sporophyte
        multicellular diploid form (2n)
        grow older and repeat the same step
        They actively move to find food
        Types
        How to
        (1) Amoebozoa
        (2) unicellular, photosynthetic species
        swimming
        drift passively in water currents
        (3) Protists with flagella or cilia
        Flagella
        long
        nine sets of doublet (paired) microtubules
        Cillia
        short
        Amoeboid motion
        crawl over a substrate
        This requires
        ATP
        actin and myosin
        Types of eating
        (1) absorb nutrients
        (3) ingesting food
        (3) perform photosynthesis
        (4) ingest food & perform photosynthesis
        produce their own organic compounds
        through photosynthesis
        They are autotrophs
        Types
        (1) single-celled organisms
        (2) giant seaweeds
        use carbon dioxide
        as their primary source of carbon
        range in size
        (1) engulf bacteria
        large protists
        (2) phagocytosis
        protists that lack a cell wall
        cell uses its plasma membrane
        to engulf a large particle
        (3) surround and ingest other protists
        or even microscopic animals
        large protists
        Types
        Possible in...
        (4) sweep protists into their gullets (mouth) with water
        (1) attach themselves to a surface
        (2) let food come to their mouth
        Unicellular protists
        nutrients are taken up directly from the environment
        through transport proteins.
        across the plasma membrane
        Types
        (1) decomposers
        eat dead organic matter
        (2) parasite
        live inside other organisms
        absorb nutrients from them
        Protists can perform very diverse way of eating!!
        Fungi (not protists)
        Animals (not protists)
        Land plants (not protists)
- Prokaryotes
  - Archaea
  - Bacteria
  - characters
    - unicellular organism
    - lacking nucleus
    - containing few organels
    - few cytoskeletal components
    - transcription and translation occur together
    - Asexual reproduction (binary fission)
BIOL213 Chp. 28
BIOL213 Chp 34

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BIOL213 Chp25~35

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