• “Evolutionary history of a species”
    • Determined through fossils, homologous structures, morphology, & molecular biology

Taxonomy: classification of organisms; organisms are classified into categories called taxa

Hierarchical Classification

  • Each taxon more inclusive than the other
  • Dumb Kings Play Chess On Fine Green Sand”
  1. Species: group of closely related organisms that can reproduce
  2. Genus: phylogenetically closely related species
  3. Family: Genera that share same features                                                                               
  4. Order
  5. Classes:
  6. Phyla:
  7. Kingdom
  8. Domain

Phylogenetic Trees

  • “Evolutionary history of an organism represented by a branching diagram” (Hypothesis!)
  • Branch Point: represents common ancestry of 2 evolutionary lineages diverging from it
  • Sister taxa: species that share immediate common ancestor not shared by other groups
    • Represents a genus
  • Basal taxon: group that diverges early on
  • Tree shows pattern of descent, NOT phenotypic similarity
  • Branch length = estimated amount of evolutionary change or time


  • Uses common ancestry and traits to place species into groups called clades                                                     
    • Clades: ancestral species & all of descendents
  • Cladogram shows relationships between diff organism from common ancestor
    • Branches determined by comparing number of derived characters in each taxon
      • More primitive = earlier branching
      • Fewer derived = later branching
    • Outgroup: species closely related but not part of the group we are studying (ingroup)
      • Is the most divergent (different) and least closely related

  • Node represents species → all three species are descended from it

Types of Clades

  • Monophyletic: ancestral species & all of its descendents (best!)
  • Paraphyletic: ancestral species & some of its descendents
  • Polyphyletic: includes distantly related species but not recent common ancestor

Shared Ancestral & Shared Derived Characteristics

  • Descent with modification has resulted in organisms with shared and diff characteristics from common ancestor
  • Shared Ancestral: character that originated from ancestor of a taxon (ex: backbone)
  • Derived: novelty unique to clade
    • Can be loss or gain of a characteristic

Maximum Parsimony: simplest explanation is usually most correct one

  • Most parsimonious tree is the one with the less amount of changes                                                               
  • This tree is less parisomus bcuz assumes that jaw evolved twice

Evolution and Genome

  • Comparison of nucleic acids can show relatedness
    • Ex: between humans and fungi
  • Diff genes evolve at diff rates = molecular trees represent short/long period of time
    • rRNA changes slowly→ investigate events that happened long time ago
    • mDNA evolves rapidly→ investigate recent events
  • Orthologous genes: homologous genes found is diff species as a result of speciation
  • Paralogous genes: homologous genes in a species that results from gene duplication
    • May diverge and take on new functions; useful cuz extra copy of genes permits modification w/o loss of original copy
    • Pseudogenes: Paralogous genes that have lost function of coding for functional gene product (vestigial) 
  • Over evolution will have high mutations
  • Nucleic acids are poorly conserved
    • Conserved = few changes over time
    • Poorly conserved homologous genes used to relate distant species

Molecular Clocks

  • “Method of estimating past evolution events based on pattern of neutral mutations”

                  Mutations in genes make it accurate and natural selections makes inaccurate