I should add that <references> is also within a template, and called using {{#tag:references}} with a series of calls to another template which calls the ref tag via the #tag parser function {{#tag:ref}}.
Incase anyone is inclined to look over the templates...
Ref template (outputs a reference in article text) http://practicalplants.org/wiki/Template:Ref?action=edit
References template (used to output the reference list) http://practicalplants.org/wiki/Template:References?action=edit
Reference template (an individual reference in the list) http://practicalplants.org/wiki/Template:Reference?action=edit