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Genomes include junk DNA. The older the species the more time it's genome has had to accumulate junk. Amoeba have been around longer than mammals.
Ahhhh the C value paradox/enigma Non-coding DNA or 'junk DNA' is only the parts of the genome that we don't as yet know the function of, it doesn't mean it's not used. Couple of reasonable linkshttp://sandwalk.blogspot.com/2007/09/genome-size-complexity-and-c-value.htmlhttp://en.wikipedia.org/wiki/C-value_enigmaI think the safest answer is that we don't actually know why, not with any definitive proof. If you really get the taste for it I can look up some published papers for you, but they are hard-going!