Question

two species with similar adaptations are found to have key differences at the molecular level. Scientists conclude that these species are not as closely related as previously thought. Why should the molecular evidence outweigh physical similarities that the species share?

Answer 1

Genetic similarities are a direct indicator of how closely two species are related. As an example, something like 90% of all genes are inactive (they have no effect on the organism). Through random mutations over time the inactive genes will drift away from each other in two species that shared a common ancestor. The rate of drift is fairly constant and can be used to estimate how many generations back two species are related.

Answer 2

The physical similarities don't necessarily mean that the two species are related. They have evolved physical structures that are like each other because they have similar needs in their environments. A cactus has spines for defense, and a hedgehog has spines for defense. In both cases, the spines work very well for defense, but this doesn't mean the two organisms are related to each other.

On the other hand, similarities in DNA mean that the two species have not been separated from each other by evolution for as long as other species that have fewer DNA similarities. The more alike the DNA is, the more closely related the two species are. DNA evidence is pretty hard to argue against.