Reading and understanding phylogenetic trees

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					    Reading and
 phylogenetic trees
 This early example of
using the tree metaphor
 implies that branches
 that are lower on the
 tree of life represent
    more “primitive”
   This is incorrect.
Basic tree notation.
•      What are phylogenetic trees?
    Nested hierarchies of sister taxon

                                         sister taxa
                                         sister taxa

                                         stem species

                                  node: an ancestral species,
                                  common to two sister taxa

                     polytomy: could be either an unresolved node, or that
                      three species were derived from a single ancestor
What are phylogenetic trees?
                Although phylogenetic trees are
                 usually read left to right, each
                      node can be rotated
                     Therefore, there is no
                  evolutionary sequence to be
                       read from the tree.
                      Because trees are made from
                characteristics of organisms, and because
                almost all taxa on trees are extant, basal
                 branches does not equal basal taxa, or
                               basal clades

             The most common error in tree
           reading is to assume that the early
          diverging taxa (i.e. at the base of the
          tree are more “primitive” than those
                       at the tips).
 Taxonomic sampling bias creates
the illusion of ancestral vs. derived

                      Krell and Cranston, 2004
  Tree shape depends on what
geological period sampling is done
  and whether extinct taxa are
         included or not.
  Basal branching does not mean primitive
             (another example)

we would not call humans primitive: we
 would refer to humans in this case as
 the sister taxon of the proteobacteria
   Another example of how
 taxonomic sampling and tree
presentation can be misleading

  which taxon is basal here?
         Natural Selection: easy to
            understand, difficult to
•   Selection is ademonstrate. to
                   catch-all word
    denote the way the abiotic and biotic
    environment creates differential
•   reproductive success.
    differential reproductive success is the
    definition of fitness. Individuals with greater
    fitness pass along those features to
•   If those features become fixed in the
    population, evolution has occurred.
•   How can we demonstrate which features of
    organisms have responded to natural

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