DIFFICULTIES IN PHYLOGENETIC ANALYSIS

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Mind Map on DIFFICULTIES IN PHYLOGENETIC ANALYSIS, created by tomking304 on 31/08/2013.
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DIFFICULTIES IN PHYLOGENETIC ANALYSIS
  1. scoring characteristics can be hard
    1. anatomical characters important in systematics - data typically only available for extinct organisms
      1. deciding number of independent character differences
        1. DNA sequence data - changes at several sites might be likely to evolve in concert to preserve function
          1. DNA sequences must be aligned so homologous sites can be compared
          2. homoplasy is common
            1. data set may yield several different phylogenetic estimates that are equally as good
              1. unwise to rely on particular phylogenetic estimate if other hypotheses imply just a few extra evolutionary changes
                1. try to get more data on other characters instead
            2. process of evolution often erases traces of prior evolutionary history
              1. is studied taxa diverged long ago or evolved very rapidly many characteristics will have diverged so much that homologous characters difficult to discern
                1. eg teeth useful for determining relationships between many mammals but can't use to assess relationship of toothless anteater
                2. earlier synapomorphies erased from DNA sequences by multiple substitutions occurring at a site
                  1. evidence of common ancestry lost if mutation occurs at site multiple times, eg A to C then C to G
                    1. more likely for same substitution to occur in parallel in different lineages as time passes
                      1. convergent evolution & successive substitutions cause amount of sequence divergence between taxa to level off
                      2. rapidly evolving DNA sequences useful for phylogenetic analyses of taxa that diverged recently
                        1. slowly evolving sequences required to assess relationships among taxa that diverged in distant past
                          1. some lineages diverge so rapidly little opportunity for ancestors of each monophyletic group to evolve distinct synapomorphies
                            1. ADAPTIVE RADIATION
                              1. evolutionary radiation associated with marked adaptive diversification
                            2. EVOLUTIONARY RADIATION
                              1. episode of significantly sustained excess of cladogenesis over extinction
                                1. CLADOGENESIS
                                  1. splitting of lineage into 2 or more descendant lineages
                              2. HYBRIDISATION
                                1. offspring from interbreeding from 2 different populations or species
                                  1. usually transfers genes between populations or species
                                2. HORIZONTAL / LATERAL GENE TRANSFER
                                  1. usually incorporates just a few genes of one species into the genome of another species (contrasts to hybridisation)
                                    1. very important in evolution of bacteria - responsible for providing genes for antibiotic resistance
                                      1. usually through viruses (natural) or genetic modification (human intervention)
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