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.