LOE - Phylogeny

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Phylogenetic trees

  • Graphical representations of evolutionary relationships (phylogeny) in a set of organisms.
  • Systematic taxonomy: Organises the diversity of living things into an evolutionary context - taxonomy/classification should reflect organismal phylogeny.
  • Early trees: Darwin's tree of life shows how a genus of related species may originate via divergence from a certain starting point.
  • Traditionally used subjective features to classify and identify relationships (e.g. visible morphologies), but now objective features are used, e.g. DNA, protein sequences.
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4 aspects of a phylogenetic tree

1. Topology - The shape of the tree.

2. Branch lengths - May be drawn to scale, to represent the inferred amount of change on the branch.

3. Root - The oldest point on the tree; the last common ancestor of all sequences on the tree. Trees are often rooted using an outgroup - an organism outside the taxa of study - to avoid needing to define the position of the root (i.e. if it is unknown).

4. Confidence - Bootstrap confidence values are assigned to each branch, to show the support for that branch. They show how many times that particular branch was found in bootstrap sample trees.

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Organismal phylogeny and classification

  • Under systematic taxonomy, classification should perfectly follow phylogeny.
  • Monophyletic groups - Consist of most recent common ancestor, and all of its descendents.
  • Paraphyletic groups - Consist of the ancestral species and some of its descendents. 
  • Polyphyletic groups - Group of organisms without a common ancestor.
  • In systematic taxonomy, paraphyletic and polyphyletic groups are invalid.
  • However, use of paraphyletic groups cannot always be avoided (e.g. class Reptilia includes reptiles but not birds), despite their use being discouraged.
  • Polyphyletic groups must be split up to form valid groups.
  • Cladistic approach to phylogenies: Phylogenies can be inferred by identifying organismal characteristics that vary among species.
  • Taxonomic hierarchies are based on shared characteristics.
  • Clades - Groups sharing derived characteristics, and they form a subset within a larger group.
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Homology and homoplasy

  • Homologous characters - Inherited directly from a common ancestor.
  • Homoplasious characters - Evolved independently in different lines, due to either convergent or parallel evolution. Can give misleading information when determining relationships.
  • Shared derived characters - A new feature unique to a particular group.
  • Primitive/ancestral characters - A shared character of multiple clades.
  • Shared derived characters are more useful when determining relationships than primitive/ancestral characters.
  • Synapomorphy - Shared derived character, e.g. Mammals have fur, and this is unique to the Mammals.
  • Symplesiomorphy - Shared ancestral character, inherited from ancestors older than the last common ancestor. e.g. all Mammals have a backbone, but so do all Vertebrates.
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