Another question that comes up is more specific, but is also an example drawn from dogs. It's frequently charged that if a palaeontologist had found the skeleton of a thylacine (or Tasmanian 'wolf' or Tasmanian 'tiger'), they would probably classify it (incorrectly) as a dog, rather than as a marsupial. The reason, we are told, is because the skeleton of a thylacine "looks like" a dog's, more than it does that of a marsupial such as a kangaroo or koala.
Here's a wolf skull. For our purposes, entirely like that of a typical domestic dog.
Now here's the skull of a thylacine
Upon first inspection, it's hard to see how a palaeontologist could possibly distinguish the two skulls. The reality is that it's very, very easy. Turn the skull over and look at the teeth. Here's dental arcade of a thylacine:
Note that there are four molars, the last three being nearly identical except in size. Now look at the tooth arcade of a dog:
One of the defining features of modern placental mammals is that they never have more than three molars. This already separates the thylacine skull not only from dogs, but all placentals. In this case, the dog only has two molars and a single premolar modified into what is called a 'carnassial' - a shear-like tooth for cutting meat. Note also that the thylacine skull has a pair of palatal fenestrae: window-like openings on the bottom of the skull, a character found in marsupials such as wombat skull. The dog skull clearly does not. (Don't confuse it with the passages seen behind the dog's palate - this is the choana, or internal nostril. The thylacine has this feature in addition to the palatal fenestrae, but it's not seen in the picture). These actually amount to only a few of the numerous differences in the skull that distinguish placental mammals from marsupials.
The fact that systemtatists and palaeontologists can identify marsupials from their bones is evidenced by the sabre-toothed marsupials. These forms look very similar to the familiar sabre-tooth cats. Despite only being known from fossils, they have been distinguished by palaeontologists as marsupial and placental carnivoran, respectively. This is because there are numerous aspects of the skull, such as dental characters discussed above, that can be used to unambiguously distinguish them. In addition to skull and dental characters, marsupials bear a prepubic bone (ofthen called the "marsupial bone") that projects forward from the front of the hips. It appears to be related to the pouch that marsupials use to carry their young. When entire skeletons are available, it serves as nother character to distinguish these two groups.
Here we see that not only would palaeontologists know how to separate the thylacine from dogs on the basis of bones alone, but that they routinely do distinguish marsupials from placentals in the fossil record. The evolutionary history of organisms is long and complex. Even if two organisms happen to take on very similar general appearance, the traces of their ancestry are often still documented by other parts of their anatomy. Palaeontologists and systematists search for these traces which are held in the shared unique characters held between members that share common ancestors - rather than relying on overt general similarities.
Just as in other sciences, common sense often betrays reality in systematics. This is not to say that reality never betrays systematics, either - it certianly can. Indeed convergence and incompleteness can frequently play havoc with the reconstruction of phylogeny (evolutionary relationships). However, sticking things together by overt similarity is not how things are done. Systematists look for nested sets of these shared unique similarities which, as we have seen with dogs and now marsupial vs. placental mammals, that are most useful in uncovering the true nature of evolutionary relationships.