Module 4: Phylogenetics

• early classification categories:

  • animalia (mobile, consumers)
  • plantae (immobile, producers)
  • protista
• 5 kingdoms classification:

  • mode of feeding (photosynthesis, absorption, ingestion)
  • unicellular/multicellular
  • bacteria/monera as common ancestor
• problems with classification before phylogeny:

  • based on observable traits
  • in bacteria morphology, size, and motility don't provide evolutionary relationship
  • metabolic properties cross phylogenetic boundaries
  • bacteria feed by photosynthesis and absorption
• phylogenetic classification: based on evolutionary relationship using genotype
• what did carl woese discover?

  archaea (3 domain concept), molecular phylogeny, 16 S rRNA
• 16 S rRNA is conserved, large, and rarely transferred horizontally (between species)
• endosymbiont: amoeba that contains cyanobacteria-like plastid
• endosymbiont ameoba and plastid are dependent on eachother
• endosymbiosis: archaea swallowed bacteria to form eukaryote
• evidence of endosymbiosis: eukaryotes have archael and bacterial components
• what archaeal components do eukaryotes have?

  • ribosomes
  • membranes
  • cytoplasmic contents
• what bacterial components do eukaryotes have?

  • mitochondria
  • chloroplasts
• what characteristics do chloroplasts (eukarya) and cyanobacteria (prokaryote) share?

  • 2 membranes
  • photosynthesize
  • circular DNA
  • 70 S (bacterial) ribosome
• distinguishing characteristics of bacteria: single celled pathogens
• distinguishing characteristic of archaea: not pathogens
• distinguishing characteristics of eukarya: sexual reproduction, simple metabolism
• why is metabolism conserved across eukaryotes?

  all driven by mitochondria
• firmicules:

  • gram +
  • pathogens
  • some form endospores
  • food production (fermentation)
• proteobacteria:

  • gram -
  • pathogens
  • related to mitochondria
• hydrogen-oxidizing bacteria:

  • H2 as e- donor and O2 as acceptor for respiration
  • can fix CO2 and nitrogen
• actinobacteria:

  • gram +
  • filamentous
  • some pathogens, some produce antibiotics
• cyanobacteria:

  • gram -
  • colonial/multicellular
  • not pathogens, produce toxins (blue green algae)
  • oxygenic photosynthesis
  • related to chloroplast
• extremophiles:

  • thermophiles (high temp)
  • halophiles (high salt)
  • acidophiles (low ph)
• methanogens: produce methane
• protists:

  • microbial
  • pathogens
• fungi:

  • absorptive heterotrophs
  • reproduce via spores
  • can cause plant disease
• fungi types:

  • yeast (single-celled)
  • filamentous (multicellular)
  • dimorphic (both)
• defining microbial species by phenotype:

  • species have similar properties
  • more common traits means more related
• why can't bacteria species be defined by phenotype?

  bacteria can lose or gain abilities and still be similar
• defining microbial species by DNA

  • 70% DNA similarity
  • 97-99% rRNA similarity
• why cant microbe species be defined by DNA similarity?

  identical rRNA can have different genes and properties
• how can identical rRNA have different genes?

  horizontal gene transfer between bacterial species, overrides classic evolutionary pathway