new ecological opportunities for Lupinus diversification (Janzen, 1967;Simpson, 1975). The phylogenetic relations within the genus are still under discussion because of lack of resolution (Käss and Wink, 1997;Hughes and Eastwood, 2006). Moreover, some species are highly variable, forming widespread polymorphic species alliances with complex infraspecific taxonomies, as exemplified by the Lupinus albifrons (Huang and Friar, 2011) and Lupinus microcarpus (Drummond and Hamilton, 2007) complexes in California and the Lupinus montanus complex (Dunn and Harmon, 1977) in Mexico, which is the focus of this study.These alliances are potential examples of incomplete speciation, in which the subspecies/varieties correspond to incipient or ephemeral species, as described by Rosenblum et al. (2012) and Levin (2005). They concluded that 3 main processes are involved in speciation, as suggested by Givnish (2010): 1) the initial origin of genetic differentiation among populations, 2) the evolution of reproductive isolation, and 3) the evolution of ecological divergence in the form of the speciation process. However,