The relationships depicted by an evolutionary tree


Logically, which of these should cast the most doubt on the relationships depicted by an evolutionary tree?
The skeletal remains of the organisms depicted by the tree were incomplete (in other words, some bones were missing).
None of the organisms depicted by the tree ate the same foods.
Transitional fossils had not been found.
Some of the organisms depicted by the tree had lived in different habitats.
Relationships between DNA sequences among the species did not match relationships between skeletal patterns. 

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Biology: The relationships depicted by an evolutionary tree
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