Have a look at https://www.dokuwiki.org/namespaces
As I understand your question you wan to have for example a namespace called genus which contains (amongst others) a page called "Felis". You also need a namespace called species within which is a page called "Felis catus". These appear to DW as
On the :genus:felis[/m] you can refer to [m][[:species:felis_catus]][/m] and on [m]:species:felis_catus[/m] you can refer to [m][[:genus:felis]][/m]. Please note the leading [m]:
, it forces the path resolution up to the top. If you're not happy with UNIX-style pathnames, and I've understood your requirements correctly, then I would seriously suggest you restrict yourself to the above.
Relative paths are possible ("up a level then come down a different route") but slightly less intuitive. The relative forms of the above two links would be: [[..:genus:felis]][/m] and [m][[..:species:felis_catus]][/m]. Relative paths are important if, for example, you want to store the ''felis'' page in user>teeber>classwork>taxonomy_project>genus>felis since the moggies are then linked to by [m][[..:species:felis_catus]][/m] rather than [m][[:user:teeber:classwork:taxonomy_project:species:felis_catus]]