Default assumptions in phylogenetics
1.The sequence is correct and
originates from the specified source.
2.The sequences are homologous (i.e.,
are all descended in some way from a shared ancestral
sequence).
3.Each position in a sequence
alignment is homologous with every other in that
alignment.
4.Each of the multiple sequences
included in a common analysis has a common
phylogenetic history with the others (e.g., there are no mixtures of nuclear and
organellar sequences).
5.The sampling of
taxa is adequate to resolve the problem of interest.
6.Sequence variation among the samples
is representative of the broader group of
interest.
7.The sequence variability in the
sample contains phylogenetic signal adequate to
resolve the problem of interest.
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