I'll just jump in here, I'm not an evelutionary biolagist but this occurs to me. The basic genes contained in all animals are the same. The same gene governs your arm and a fly's wing. That surely is compelling evidence of a common ancestor.

Now, take a snake for example. The snake has the genes to create legs but it's genome switches the gene off on every vertebrae and they all register a chest cavety with ribs instead but should the switch be flicked back on the snake could have ten legs.

Look at Coyotes and Wolves, virtually the same genetically, they must have a common ancestor, if evolution is true, they look different but genetically the difference is close to nill. So maybe in looking at the record you need to fuzz the definition of species to see the crossover.