It could any of those, or keywords and sub-keywords.
If your organization is as simple as you describe ... a single hierarchy of bird species, then I really don't think it matters. If they come over from Aperture as folders and subfolders (I don't really know if that's what happens when you transfer from Aperture), I would leave them as folders and subfolders.
If your organization is somewhat more complicated than what you described, then I would use keywords.
In LR would the Avocets category be classed as a Folder or Sub Folder and the Water Birds as a Collection Set?
It seems like you are confusing folders with collections, these are unrelated to one another and you cannot have a hierarchy of folders or subfolders inside a collection set.