A phylogeny of the same taxa based only on morphological traits:
Some highly conserved genetic sequences can result in unrelated species appearing closely related in a molecular phylogeny, and not reflect the same pattern as the morphologic phylogeny.
Gene sequence changes may not result in morphological changes.
Gene sequences always provide more data than morphological traits.
Morphological analyses always provide more data because each morphological trait is the result of the expression of many genes.
The molecular data may be based on the analysis of introns, which aren't expressed and don't contribute to the evolutionary history of a group of taxa.
Why is molecular data more accurate?
Phylogenetic trees reconstructed from molecular sequences are often considered more reliable than those reconstructed from morphological characters, in part because convergent evolution, which confounds phylogenetic reconstruction, is believed to be rarer for molecular sequences than for morphologies
Survival of the fittest. If one organism thrives better in an enviornment and the other organism struggles, the one that is more adapted will obviously play a part in helping the less adapted organism die out. Food is a major point along with other aspects
