phylogeny, biodiversity, plants, animals

• Structure of phylogenetic trees

  
• How phylogenetics help us to answer biological questions about how organisms evolved

  
• Taxonomy


  Ordered division and naming of organisms
• Phylogeny


  Evolutionary history of a species or group of related species
• Systematics


  Scientific discipline of classifying organisms and determining their evolutionary relationships

  
• Hierarchical classification


  • Carolus Linnaeus (1735) published a system of taxonomy grouping species into increasingly broad categories
  • Major taxonomic groups from broad to narrow are: domain, kingdom, phylum, class, order, family, genus and species

  
• Binomial nomenclature


  • Species are assigned a two-part scientific name: Genus and Specific epithet
  • First letter of genus is capitalized, and the entire species name is italicized
• Linking classification and phylogeny


  • The Linnaean taxonomic system can (sometimes) be mapped on to phylogenetic trees
  • Phylogenetic tree: a hypothesis about the evolutionary relationships between taxa
  • Organisms are often reclassified as more evidence is discovered

  
• Taxa are more closely related the more recently in time they share a common ancestor (the more recently in time they have diverged)

  
• • Phylogenetic trees show patterns of descent (speciation history), not necessarily phenotypic similarity
  • Phylogenetic trees may or may not indicate how much morphological or molecular change has occurred in a lineage
  • Branch lengths may or may not indicate absolute time
  • It should not be assumed that a taxon evolved from the taxon next to it

  
• Cladistics


  • System of constructing phylogenetic trees using shared characters and inferred common ancestry
  • Clade: group of species that includes an ancestral species and all its descendants

  
• Ancestral versus derived characters


  • Shared ancestral character: character that originated in an ancestor prior to the clade of interest; ancestral state
  • Shared derived character: character that is novel to a particular clade (Synapomorphy)

  
• Phylogenies can be constructed using anatomical, developmental, and molecular homologies
• Ingroup


  Species or group of species being studied in a phylogenetic analysis

  
• Outgroup


  Species or group of species that is closely related to the ingroup, but diverged before the ingroup

  
• • Phylogenetic trees are hypotheses
  • Multiple phylogenetic trees can be constructed for any groups of organisms
  • The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil
  • Phylogenetic trees are subject to change with new data

  
• Phylogenies can help us make predictions
• Molecular clock


  • Using constant rates of mutation to estimate divergence times
  • Assumption 1: the number of nucleotide changes between two species is proportional to the time of their initial divergence
  • Assumption 2: the rate of nucleotide changes is constant
  • Molecular clocks are calibrated using fossils
• • In 1977, Carl Woese introduced the three-domain system: Bacteria, Archaea and Eukarya
  • Three-domain system supported by data from many sequenced genomes

  
• • The "tree" of life may be more like a tangled "web" of life
  • Prokaryotic "species"
  • Horizontal gene transfer
• Taxon: a taxonomic unit at any level of hierarchy