In the scientific community, the theory of evolution is widely accepted as fact. The theory of evolution suggests that closely related species evolved from a common ancestor to suit their slightly different environments, and therefore structurally similar animals would be more closely related than behaviourally or apparently similar animals.
For example, in the animal kingdom, bright colours often indicate 'I'm poisonous. Don't eat me.' Some animals that are not poisonous take on the same colours and therefore avoid predation. They look identical to the poisonous species, but are often not even members of the same family.
Also, species that exploit the same niche and therefore behave in the same manner may be totally different to each other. Nobody would class a horse and a deer in the same family, but they are both medium to large herbivores that live in groups and prefer to flee than fight when threatened. This is behavioral similarity.
If scientists classify animals by physical or structural similarities, it is easier to sort, index and classify using a set of logical scientific names than if they attempt to sort them any other way. Often it is done differently in 'layperson's terms'. ie. Dog breeds are often sorted based on size, region of origin or use ('Toy' breeds, Germanic-origin breeds, gundogs breeds) although all domestic dogs are the same species.
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