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Life on Earth (Phylogeny (Shared characters are used to construct…

- - - - Use of scientific discipline of taxonomy
      - Binomial nomenclature
        
        introduced to eliminate language barrier
        
        brought in by Carolus Linnaeus
        
        first part of binomial is genus
        
        second is species
      - Hierarchical Classification
        
        DKPCOFGS
        
        named taxonomic unit at any hierarchy called taxon
  - - - What to learn from phylogenetic trees
        
        Represents hypothesis about evolutionary relationships
        
        relationship depicted as branch points
        
        represents common ancestor of lineages that diverge
        
        Each tree has branch point that shows common ancestors
        
        Chimps and humans are considered sister taxa
        
        groups of organisms that share common ancestor that nobody else shares
        
        all trees are rooted
        
        a branch point within tree represents most common ancestor of all taxa in tree
        
        linage that diverges early is called basal taxon
        
        Intended to show patterns of descent not phenotypic similarities
        
        Can't infer ages of texa or branch points
        
        Should not assume that taxon evolved from taxon next to it
  - - - identification of two species of grass that might be maize's closest living relatives
      - may be useful as reservoirs of alleles that can be transferred to cultivated maize
    - - by analyzing relatedness of DNA sequences from different organisms
  - - - phenotypic and genetic similarities due to shared ancestry - homologies
        
        organism that share similar morphologies are likely to be more related than org w/ diff structures
    - - source of confusion is convergent evolution
      - complexity of what's being compared is a clue
        
        more parts that are similar, more likely that it evolved from a common ancestor
        
        Same with comparisons at gene level
  - - - approach to systematics where common ancestry is primary criterion to classify organisms
      - place species in clades
        
        taxonomic categories of Linnaean syst that are nested within larger clades
    - - consists of ancestral species and all descendants
    - - consists of ancestral species and some, not all, of its descendants
    - - includes distantly related species but not most recent common ancestor
    - - character that originated in ancestor of of taxon
        
        e.g. backbone because it predates branching of mammals, therefore it's shared for mammals
    - - evolutionary novelty unique to a clade
        
        e.g. hair bc its shared by all mammals but not found in ancestors
        
        can indicate a loss of a feature as well
    - - proportional to amount of evolutionary change or to times where particular events occurred
    - - simplest explanation that's consistent with facts
        
        Think of Occam's razor
    - - Identifies the tree that most likely produced a given set of DNA based on certain rules
    - - hypothesis could be modified with new evidence
  - - - duplication increases number of genes in genome and more opportunities for evolutionary change
        
        Two types of homologous genes
        
        Orthologous
        
        homology is result of speciation event and occurs between genes foud in differnt species
        
        Paralogous
        
        homology results from gene duplication
        
        copies of these genes diverged within a species
    - - lineages that diverged long ago share many orthologous genes
      - number of genes a species has doesn't seem to increase through duplication at the same rate of perceived phenotypic complexity
  - - - can be explained by neutral mutations
        
        harmful mutations are removed quickly
        
        neutral mutation rate is like clockwork
        
        explained by how important a gene is
    - - certain changes are favored
      - molecular clocks only been used to date evol. divergences a long time ago, assuming that clocks were constant at the time
  - - - eukaryotes can get nuclear genes from bacteria and archea
- - - - based on decay of radioactive isotopes
      - old fossils with little C-14 can't be dated
  - - - changes took a long time to occur
        
        changes occurred in steps
      - have anatomical features that fossilize readily
        
        ear bones
        
        lower jaw is one bone
        
        different parts of teeth
  - - - First 3 Hadean, Archaean, Proterzoic - lasted 4 bil yrs
      - Latest- Phanerzoic (0.5 bil yrs)
        
        encompasses most of time of animal existence
        
        divided in 3 eras
        
        Paleozoic, Mesozoic, and Cenozoic
      - Breakdown
        
        First single-celled organisms
        
        3.5 bil yrs ago
        
        fossilized stromatolites
        
        layered rocks that form when prokaryotes bind thin films of sediment
        
        Photosynthesis and O2
        
        first O2 produced dissolved in water
        
        oxidized iron
        
        precipitated then formed sediments
        
        O2 gassed out and entered atm.
        
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        First eukaryotic cells
        
        originated by endosymbiosis
        
        engulf cell that evolve into organelles
        
        serial edosymbiosis
        
        mitochondria evolved before plastids
        
        Multicellularity
        
        earliest taxanomically recorded are red algae
        
        older fossils are small eukaryotes
        
        before Edicaran period, everything was microbial
        
        Cambrian Explosion
        
        most present day phyla suddenly appeared in fossils
        
        before this, all large animals were soft-bodied
        
        Colonization of land
        
        plants colonized land in company of fungi
        
        roots took time to become an adaptation for plants
        
        Arthropods were one of the first animals to colonize land
- - - - called paedomorphosis
- - - - this assumes that only complicated eyes are useful
- - - - Defines boundary between Paleozoic and Mesozoic eras
        
        claimed about 96% of marine animal species
        
        terrestrial life affected too
    - - Extinguished more than half of all marine species
      - eliminated many terrestrial creatures including all dinosaurs
      - Possible cause is iridium from meteorite that made a cloud that blocked sun
    - - 3rd largest
      - affected most life at sea
      - Cause: drop in CO2
    - - Life in shallow seas most affected
      - Cause: asteroid/ massive flood of lava/ drop in O2
  - - - messing everything up
  - - - Adaptive radiations
        
        periods of evolutionary change to fill in different ecological roles
        
        large scale radiations occurred after each extinction
        
        Worldwide adaptive radiations
        
        history of life greatly altered by radiations
        
        organisms that arise can serve as a new source of food
        
        Regional adaptive radiations
        
        can be initiated when few organisms go to a new location w/ little competition
        
        Hawaii is great example
- - - - Simple cell creation sequence
        
        Joining of the small molecules into macromolecules (proteins & nucleic acids)
        
        Packaging of those into protocells
        
        Protocell- droplets with membranes that had different chemistry inside than surroundings
        
        Self-replicating molecules & metabolic source of building blocks appear #
        
        First genetic material is RNA not DNA
        
        Plays role in protein synthesis
        
        Can function as enzyme-like catalyst
        
        Ribozomes
        
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        Self-replicating molecules made inheritance possible
        
        Abiotic synthesis of amino acids and nitrogenous bases
    - - Planet formed 4.6bil yrs ago
        
        Initially bombarded by leftover ice and rock
        
        First atm. little O2 heavy H2O vapor
        
        Volcanic vapors released into atm.
        
        Earth cooled and H2O condensed to make oceans
        
        H2 escaped to space
        
        Early atm. made up of nitrogen and CO2 w/ no redox
        
        Small pockets of of early atm. near volcano has redox
      - Miller-Urey Experiment
        
        Tried to create conditions like early Earth
        
        Produced amino acids and organic compounds
        
        Similar experiments used neutral atm. #
      - Hypotheses
        
        organic compounds produced in hydrothermal vents
        
        areas on seafloor where heated water and minerals flow in ocean
        
        alkaline vents
        
        high pH (9-11)
        
        warm water instead of hot
        
        abiotic synthesis of org. molecules possible in diff. conditions
        
        Murchison meteorite
        
        4.5 bil yr old rock landed in Australia
        
        contained 80 amino acids not from Earth
      - Abiotic synthesis of macromolecules
        
        abiotic synthesis of RNA monomers can occur from precursor molecules
        
        dripping son of amino acids or RNA nucleotides to hot sand produce polymers
        
        polymers produce w/o help of enzymes or ribosomes
      - Protocells
        
        self-replicating molecules & metabolic source appeared
        
        conditions might've been met in vesicles
        
        abiotically produced vesicles can exhibit properties of life
    - - first genetic material
      - play role in protein synthesis
      - can function as enzyme-like catalyst
        
        called ribozymes
        
        make complimentary copies of short pieces of RNA
      - could have provided template where DNA molecules are assembled