How to incorporate intraspecific variation in discrete characters in comparative analyzes?
Kostikova et al. 2016. Syst. Biol. developed an algorithm to model trait evolution with inter- and intraspecific variation. The authors use it to show 


  whether a life-history trait (i.e. annual versus perennial) influences the evolution of intraspecific variation in the climatic niches of species


While they do not directly incorporate the space component as in the RLQ analysis, the approach might be informative in your case. The functions are available through dryad.