The humans have been around for a few million years, other organisms longer yet. Changes that occur in the genome and propagate (may) eventually throw a new species ... or atleast branch off the old one. Are there any chromosomes out there that may be more susceptible to mutation than their neighbours?
terdon is spot on with the recombination hotspot comment. Mutations are often associated with recombination (information gets lost during crossing-over, so DNA repair is necessary, which of course can introduce mistakes/mutations). It's a fact that there areas in certain chromosomes where recombination happens much more often than other areas of the chromosome. So it follows that chromosomes with more hotspots would likely have higher mutation rates than other chromosomes, on average. This does raise the point, though, that perhaps it's not the mutation rate of the entire chromosome that matters-maybe mutation rates at a more-local level (such as near a hotspot or far away from a hotspot) are more worthy of consideration for your question. Also, I imagine that sex chromosomes have much lower levels of polymorphism than autosomes. This doesn't have to be because of a lower mutation rate, though: another explanation would be that deleterious recessive mutations on the X chromosome would be purged more easily than on autosomes because their phenotype appears in males (who don't have a second allele because they don't have another X chromosome, so the deleterious phenotype can't be "hidden" like it would in a heterozygote).