One of the best "smoking gun" pieces of evidence of humans' close relation to chimpanzees, gorillas and orangutans is that human chromosome 2 is a fusion of two primate chromosomes, with a double telomere in the middle and a centromere on each side. This fusion, which occurred some time after our MRCA with chimpanzees, was an accident with no evolutionary importance, but it happens to provide extra support for our common ancestry with other African apes. In theory, such fusions could be so commonplace that they can be used to infer much of the family tree of life on their own. I'm sure they're nowhere near that common, but this got me thinking: are there any other examples of species with chromosome fusions (or splittings?) that betray their closest relatives?
You can go to ensembl.org and look up synteny between closely related organisms, like rats and mice. Below is one example: rat chromsome 1 is made up of all of mouse chromosome 7 and 19, plus parts of 17, 10, and a smidge of 13