There are various concepts of ‘species’, and they are not entirely incompatible; they simply emphasize different ‘aspects’ of species. Mayr’s BSC (Biological Species Concept) emphasizes that reproductive isolation is what keeps sexual lineages on the tree of life separated from one another.
For many geneticists, the BSC is the preferred description of species because it emphasizes reproductive isolation between species.
The BSC has its drawbacks as well. For instance, it cannot be applied to organisms that are extinct(fossil species) or species that reproduces asexually(like prokaryotic organisms).
There are plenty of prezygotic barriers that can exist within a species, though. Birds are known for having a variety of regional dialects that prevent mating. White-crowned sparrows, for instance, populate the entire United States but plenty of research has been done illustrating how birds from the west and east won't recognize each other's songs. Dialects can form in much smaller regions too, especially if ranges are small or the two populations are separated by a geographic or different zygote barrier such as breeding out of phase.
Side note because it's cool: ring species. The best-documented example of a ring species is the Ensatina eschscholtzii (no real common name), which is unique because its low vagility has formed a number of different subspecies as it populates the coastal and Sierra mountain ranges of California. Starting from the top, each subspecies can breed with its neighbors, but once you reach the bottom of the ring the two subspecies that meet there cannot interbreed. It's kind of awesome.
Basically, the definition of "species" within the scientific community is starting to be in flux. "Lineages" is probably a good alternative.
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Anyways, if I were to make a phylogeny of the different races in One Piece I'd probably use dwarves as an outgroup, then fishmen/merpeople, minks, giants, humans, and finally Longarms and Longlegs. We'll never find out anyway so who cares if it's right?
Though actually, we've never seen a Longarm or Longleg hybrid. Hmmmm.....