What is a refuge tree? What is the nature of a refuge tree(s)?  How does one incorporate a refuge tree(s) into their practice?
My understanding of a refuge tree is a visual representation of a lineage of a particular school of Buddhism. From Wikipedia


  the lineage of gurus and transmission of teachings is depicted in
  visual form as a visual mind map


For instance I practice with the Triratna Buddhist community and we have our own refuge tree (shown below). At the bottom is Sangharakshita winding its way to his teachers (e.g. Dhardo Rimpoche) and up to more historical figures (Hakuin, Milarepa) and into the mythic (Amitabha, Ratnasambhava) up to the Buddhas past present and future (Shaykamuni, Dipankara, Maitreya).



We study it to find inspiration and guidance in other teachers and other times. Because the movement is electic it means something to us to study a Zen figure (Hakuin) and then a Tibetean (Milarepa) and draw out the underlying themes. More pragmatically and politically the Triratna Community has been criticised for lacking a proper lineage so we (over)compensate by having a refuge tree that we study and refer back to.