Verified answer

This particular definition of species doesn't apply to organisms that primarily reproduce asexually, like bacteria. Species designations are even fuzzier for them than they are for macroscopic organisms. I've heard a rule of thumb that bacteria can be considered different species if their DNA is less than 80% identical, but (A) that's obviously a completely arbitrary cutoff, and (B) by that rule, several well-established species differences, like that between E. coli and Shigella (IIRC) would have to be eliminated.

Most species, whether they are sexually reproducing or clonal, are identified morphologically. The reasoning is that it is extremely unlikely that 2 different species are almost identical morphologically due to convergent evolution. Some species resemble others closely (e.g. the marsupial wolf and the placental wolf) but if one looks closely enough, one can find differences. The marsupial wolf for example have marsupial characters not found in placental mammals.

A new species of clonal species therefore can be identified if it has evolved to be morphologically different from its ancestor. Morphology is important because it is adaptive. New species evolve because of adaptation to a different niche. Therefore new species can be identified by identifying these new morphological traits that enable the new species to adapt to the new niche. Of course, there will always be disagreement among scientists as to whether 2 populations are the same species or not. These agreements are not limited to sexually reproducing species.