Dredge, you quote:
"Furthermore, phylogenetic trees based on a certain anatomical feature will often contradict a tree based on a different anatomical feature."
" [...] In point of fact, there exists no such thing as 'the traditional textbook phylogeny'. A diversity of different schemes can be found."
... and go on to say:
If common ancestry is the reality, such contradictions should not exist and different forms of evidence should all point to one, unambiguous phylogenetic tree.
What you forget is that humans are fallible, scientists not excepted. Phylogenies are not the absolute truth, they are man-made approximations of the relatedness of life at various levels in the supposed 'tree of life'. So it is not surprising that contradictions sometimes occur in the endeavour to create a complete and accurate picture of the phylogenetic tree.
However, there is a great amount of overlap between a multiplicity of attempts at building a complete picture. And that's just in the area of phylogenetics proper. With the inclusion of relatively new evidence such as DNA-sequencing and other molecular techniques, the picture becomes ever more consistent. You are right in saying that different forms of evidence should all point to one, unambiguous phylogenetic tree. Increasingly, all the evidence combined does exactly that.
"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.
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