PHYLOGENETICS

• Phylogenetics

  The study of evolutionary relationships among a group of organisms

  
• Understanding biological evolution

  1. Inheritance through change

  2. Within a species - evolution through genes

  3. Between species - evolution from a common ancestor
• Phylogenetic tree

  A branching diagram showing the evolutionary relationships among various species based upon similarities or differences in physical or genetic characteristics

  
• Goals of Phylogenetics

  • To recreate the ancestor-descendent relationships among the species

  
• Phylogenetic trees are extremely useful tools used by taxonomists to understand

  • Composition of genomes
  • Relationship among genes in species
  • Historical relationships among diverse species
  • Origins of remarkable abilities in living organisms

  
• Phylogenetic relationships can be based on


  • DNA
  • RNA
  • Molecular markers (SNPS)
  • Chemicals compounds
  • Morphology

  
• DNA molecules

  • Cytosine [C]
  • Guanine [G]
  • Adenine [A]
  • Thymine [T]

  
• Types of DNA

  • Nuclear - transmitted from both parents
  • Chloroplast - transmitted paternally
  • Mitochondrial
• Chloroplast DNA

  • Chloroplast Gene (plastome) - easier to PCR due to the number of copies in a cell
  • Intergenic Space - high degree of variability than some coding region
• Nuclear DNA

  18S-26S Nuclear ribosomal cistron - Internal transcribed spacer (ITS), External transcribed spacer (ETS) - Effective at lower taxonomic levels

  
• DNA sequencing - PCR

  1. Denature

  2. Annealing

  3. Extension

  
• DNA sequencing methods

  • Sanger Sequencing
  • High-throughput sequencing
  • Whole genome sequencing
  • Reduced representation sequencing

  
• Different bioinformatics methods are needed for different sequencing approaches

  
• Phylogenetics can be done using both morphology and molecular data
• Biogeography is important in selecting an outgroup for phylogenetic analysis
• Physical traits


  Characteristics of an organism that can be observed with the naked eye
• Genetic traits


  Characteristics of an organism that are determined by its DNA
• Evolutionary relationships


  The connections between organisms that share a common ancestor
• Phylogenetic tree


  A diagram that depicts the evolutionary relationships among a group of organisms
• Phylogeny


  The evolutionary history or relationship of a group of organisms