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In this paper, we develop a five-step approach for analysis of historical relationships among areas of endemism using a set of 22 clades (9 mammal, 7 bird, 4 reptile, 1 amphibian, and 1 cactus) drawn from the warm deserts biota of western North America. As has been suggested in previous studies of portions of this biota, our results suggest a complex biogeographic history, but with substantial support for the influence of several major vicariant events in the diversification and assembly of the aridlands biota. We discuss and demonstrate the reciprocal strengths (and weaknesses) of phylogeography and phylogenetic biogeography for defining areas of endemism, analysing vicariance and dispersal, and dealing with temporal and spatial pseudo-congruence.