A3.2

• Tools used to classify organisms into taxonomic groups

  Cladistic methods
• Cladistic methods


  Differ from traditional taxonomic methods
• The images are both cladograms
• Cladograms show the statistical similarities between species based on their DNA/RNA
• The cladogram on the left shows bacteria classified using the 16 S ribosomal RNA gene
• The cladogram on the right uses retroviral sequences which have been incorporated into ape DNA and then inherited to build a picture of the relationships between apes
• Humans have around 100,000 endogenous retroviruses incorporated into their DNA
• Need for classification of organisms

  Classification is needed because of the immense diversity of species. After classification is completed, a broad range of further study is facilitated.
• Difficulties classifying organisms into the traditional hierarchy of taxa

  The traditional hierarchy of kingdom, phylum, class, order, family, genus and species does not always correspond to patterns of divergence generated by evolution. A fixed ranking of taxa (kingdom, phylum and so on) is arbitrary because it does not reflect the gradation of variation. Cladistics offers an alternative approach to classification using unranked clades.
• Advantages of classification corresponding to evolutionary relationships

  • The ideal classification follows evolutionary relationships, so all the members of a taxonomic group have evolved from a common ancestor. Characteristics of organisms within such a group can be predicted because they are shared within a clade.
• Clades


  Groups of organisms with common ancestry and shared characteristics. The most objective evidence for placing organisms in the same clade comes from base sequences of genes or amino acid sequences of proteins. Morphological traits can be used to assign organisms to clades.
• Molecular clock


  The gradual accumulation of sequence differences as the basis for estimates of when clades diverged from a common ancestor. This method can only give estimates because mutation rates are affected by various factors.
• Basis for constructing cladograms


  Base sequences of genes or amino acid sequences of proteins. Different criteria for judgement can lead to different hypotheses, and parsimony analysis is used to select the most probable cladogram.
• Analysing cladograms


  Students should be able to deduce evolutionary relationships, common ancestors and clades from a cladogram. They should understand the terms "root", "node" and "terminal branch", and that a node represents a hypothetical common ancestor.
• Using cladistics to investigate whether the classification of groups corresponds to evolutionary relationships

  A case study of transfer of plant species between families could be used to develop understanding, but students are not required to memorize the details. Students should appreciate that theories and other scientific knowledge claims may eventually be falsified, as in the example where similarities in morphology due to convergent evolution rather than common ancestry suggested a classification that has been shown to be false by cladistics.
• Classification of all organisms into three domains using evidence from rRNA base sequences


  This is the revolutionary reclassification with an extra taxonomic level above kingdoms that was proposed in 1977. The three domains are Archaea, Bacteria (Eubacteria), and Eukaryota.
• Natural classification groups together species that share a common ancestor from which they evolved, following the Darwinian principle of common descent.
• Artificial classification groups organisms together based on shared characteristics that do not reflect evolutionary relationships, such as the ability to fly.
• Natural classification is not straightforward due to convergent evolution and adaptive radiation.
• Dichotomous keys can be used to identify species by placing them with the most closely related species, genus, family or phyla using natural classification.
• Biochemical analysis of DNA/proteins can help overcome issues with traditional classification based on morphology/behaviours, and has resulted in species being reclassified into different families.
• The revision of the classification system to include three domains (Archaea, Bacteria, Eukaryota) based on ribosomal RNA evidence led to a paradigm shift in biology.
• Woese's work


  Discovered that organisms fall into three distinct groups
• Classification of all organisms

  • Into three domains using evidence from rRNA base sequences
• Three domains


  • Bacteria
  • Archaea
  • Eukaryota
• No one of these groups is ancestral to the others, and each shares certain features with the others as well as having unique characteristics of its own
• Bacteria and the Archaea are as different from each other as either is from the Eukaryota, the third domain
• Revision of the classification system

  Lead to a new level of taxon called domains
• Paradigm shift


  When a new theory replaces an old one by the discovery of new information
• Archaea


  • Sulfolobus sp. grow in volcanic springs
  • Halobacterium sp. lives in water with high salt concentrations
• Bacteria


  • Staphylococcus aureus can cause skin infections and respiratory disease
  • Cyanobacteria sp. are photosynthetic
  • Rhizobium sp. live symbiotically with plants and fix nitrogen
• Eukaryota


  • Includes several kingdoms including fungi, animals and plants. Examples range from algae to Humans
• Clade


  Groups of organisms with common ancestry and shared characteristics
• Cladogram


  • Tree diagram showing the similarities and differences between different species
  • Mostly based on DNA base sequences or the amino acid sequences in a protein
  • Branching points (nodes) denote a speciation event when a common ancestor splits into two, or more, species
• Cladograms can show different relationships between species depending on the DNA/amino acid sequences used in the analysis
• Molecular clock


  The rate at which mutations occur can be used to calculate how long ago species diverged
• If the DNA base sequences of two species are similar

  Then few mutations have occurred and the species only diverged relatively recently
• Mitochondrial DNA


  Has been used to construct cladograms between humans and primates
• Mutations in DNA that persist and are inherited occur at a predictable rate
• Cladogram


  The length of the lines separating species often represents the estimated time since they diverged