Speciation is an evolutionary process that gives rise to new species from pre-existing ones.
What this implies in science fiction is that ==all of the sci-fi aliens that we know had ancestors==, unless the species itself is the progenitor of all life.
But speciation is a long process (on Earth, it normally takes at least a million years) and requires reproductive isolation or the inability of two formerly intermingling and reproducing populations to keep on mating.
Usually, that’s due to a geographical barrier that physically separates them, which is the mode of speciation called allopatric (allo = different, patric = land). In many of these shared universes, allopatric speciation may explain why so many humanoid species look alike; they probably shared ancestors and just evolved separately because they were separated by space!