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Biological Diversity (Phylogeny (Biological Classification (Phylogenies…

- - - - Increases # of genes in genome
      - Compares rRNA
      - Phylogenies account for similarities that result in gene families
      - Orthologous Genes Homology resulting from same place, different organism
      - Paralogous Genes: Same gene in different location
    - - Lineages diverged long ago share orthologous genes
      - Organisms share many biochemical pathways
      - number of genes a species has doesn't occur at the same rate as what we can physically see
  - - - Homology: Similar structure, similar species
      - Any morphological divergence can be great but genetic divergence is small
    - - Analogy: Similar structure, different species
      - Animals adapting to same environment tend to have similar structures
      - Convergent Evolution
    - - Bioinformatics uses gene sequence
      - Molecular systematics uses molecular structure
  - - - Uses average rate of evolution of certain genes/genomes to fill in the blanks that fossils can't give us (origin of HIV)
      - Mutations that are harmful to survival rate happen at a slower rate b/c those organisms die
      - Mutations that are neutral happen at a faster rate b/c mutation doesn't cause the animal to die
    - - Researchers extend clocks beyond the info they have
      - Assuming that the evolutionary change is going to happen around the same time
      - Evolutionary change could be abrupt due to environmental change
  - - - Genus: 1st letter capitalized
      - Species: unique for each species
    - - Phylogeny Tree: Evolutionary history of a group of organisms
      - Hypothesis about evolutionary relationships
      - Each branch comes from common ancestor
      - Shows patterns of descent, not phenotypic similarity
      - Analyze related DNA sequences to identify them
- - - - 4 bya
      - Increase in oxygen
      - Prokaryotes appear
      - Stromatalites
    - - 2.5 bya
      - Porifera, Cnidaria
      - Oldest fossils of eukaryotic cells
      - Endosymbiosis: prokaryotic cell eats small cell and uses it
    - - .5 bya
      - Bony fish, tetrapods, reptiles, origin of insects
      - Amphibians dominant
    - - 252 mya
      - Crataceous, Jurassic, Triassic
      - Dinosaurs are abundant and diverse
    - - 66 mya
      - Mammals, birds, insects
      - Ice Ages
  - - - Continents floating above lava
      - Pangea was last super continent, every 300-500 million years. 3 main supercontinent
      - When land moves, organisms adapt or become extinct
      - Explains why extinct organisms are found in completely different areas
    - - 5 Mass Extinctions
        
        1st: 444 MYA
        
        2nd: 359 MYA
        
        Permian Extinction: 252 MYA, caused by volcanic eruption
        
        4th: 201 MYA
        
        Cretacious Extinction: 66 MYA, caused by meteorite
      - Disruptive changes to environment causes rate of extinction to increase
      - Extinct when habitat destroyed, or environment changes
      - Takes 5-10 million years for diversity of life to recover
    - - Adaptive Radiations: Periods of evolutionary change where organisms form new species and their adaptations let them fill roles in their communities
      - Happens after mass extinctions
      - Also occurs in groups that have major evolutionary advancements
      - Organisms in adaptive radiations are food for new organisms
  - - - Chunks of rock and ice created water vapor (seas and lakes)
      - Earth cooled, more water vapor condensed, more hydrogen
      - Atmosphere was electron-adding, organic compounds form simple molecules
      - Energy from lightning and UV
      - Oceans a primitive soup
      - Urey/Miller
      - Hydrothermal Vents: Area on seafloor producing dark, hot, oxygen-deficient environment
    - - Every cell has enzymes, proteins, nucleic acids
      - Synthesis can occur w/o enzymes or ribosomes
      - Occur by dripping amino acids or RNA nucleotides onto hot sand, clay, or rock
      - Possible that polymers are weak catalyst for chemical reactions
    - - Self-rep molecules + metabolic source of building blocks in early protocells
      - Early membranes proud chemical compounds
      - Vesicles form when lipids are added to water
    - - DNA is double stranded and only forms helix but RNA is single stranded and can take many shapes
      - Certain shapes make them replicate faster
      - RNA could split and pass RNA to its daughter cells (protocells)
  - - - Determine placement of basic features
      - Helps develop structures where they go
    - - Caused by mutation
      - Limited to one cell type
    - - Development of reproductive organisms is accelerated compared to other organs
      - Produces animals different from ancestors
    - - Separates species with similar species
      - Divergence of crustaceans and insects
      - Changes in nucleotide sequence
    - - Evolutionary change in rate and timing of development events (super tall)
      - Organisms shape depends on growth rates of different body parts, changes alter adult form