The snout is just the most visible feature. If you look at them carefully they are different colors, their eyes are placed differently in the skull, their shells are different, the body have different shape, etc. Although these are more subtle then the snout shape. Saying that the only difference between crocodiles and alligators is the snout is like saying the only difference between humans and gorillas is the body hair.
Here’s an analogy: How come I can’t take half the parts from a Honda Accord and half the parts from a Ford Fusion, and build a working car? They’re both 4-door sedans, and the only difference between the two is the brand on the front, right? Unfortunately, no. Even though both of them are trying to do the same job of “be a car”, and they both are based on the same original car (Model T or something similar), they’ve been gradually accumulating differences ever since they both split. Each of their new years’ models are based off making changes to their own previous model. Similar structure, but a lot of small differences means that most of their parts are probably not compatible without a lot of tweaking and customization.
In genetics there are concepts of genotype and phenotype.
**Phenotype** refers to how creatures *look* – on the basis of the instructions contained in their genetics. The expression of their genes.
**Genotype** refers to what the actual genetic information (DNA) contains. The code or blueprint for the animal if you will.
The alligator and crocodile are *phenotypically* very similar – they look like the same thing with a few minor differences.
*Genotypically*, they are too different to interbreed. That is to say their genetic code is too distinct from each other, or is organized in incompatible ways.
Reproduction in animals happens by mixing half the mother’s DNA with half the father’s DNA. The way this actually happens is DNA is broken up in to bundles called chromosomes, each offspring should have 2 copies of each chromosome, and they get one copy from their mother and a second copy from their father.
If the number of chromosomes does not match or the way the genes are organized into each chromosome are significantly different, this may have no chance of working. All the general rules we expect for how genetics works, i.e. hair color may be a mix of the parent’s hair color but eye color default to brown over blue unless *only* blue genes are present (blue is recessive) only behave in these predictable ways because each organism has 2 sets of different but *equivalent* genes organized in a similar way from each of their parents. Try to mix animals with totally different structure and organization of their genes, and you either get weird unexpected behavior or things just do not work and you cannot get living offspring.
First thing, that in biology if something looks similar, doesn’t necessarily mean that they are close *enough* to hybridize. Sometimes the *seemingly close* is not close enough. Partially because how we decide what is close, is based on superficial traits: shape, size, color etc. In biology, the internal structure is much more important. But you can’t see that from the outside.
Second thing is that snout difference is not the only difference. Snout shape is a *discriminative feature*. It means that it’s something easy to see, easy to learn, easy to teach to children etc. There are many more hard to see differences.
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