Final answer:
Organisms are ordered in a phylogenetic tree based on morphological, molecular, and fossil evidence, which collectively help determine their evolutionary relationships.
Step-by-step explanation:
The three types of characteristics used to order organisms in a phylogenetic tree are morphological (physical traits), molecular (genetic and biochemical characteristics), and fossil evidence. Morphological characteristics refer to the physical structures and forms present in the organism, which can reveal shared ancestry but can also be misleading if not combined with molecular evidence. Molecular data includes DNA and RNA sequences which provide a robust framework for determining evolutionary relationships based on genetic similarities and differences. Fossil evidence can give insights into the morphology and sometimes molecular characteristics of long-extinct organisms, aiding in placing them accurately within the tree.