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Premise of the study: A recurrent explanation for phylogeographic discontinuities in the Baja California Peninsula and the Sonoran Desert Region has been the association of vicariant events with Pliocene and Pleistocene seaway breaks. Nevertheless, despite its relevance for plant dispersal, other explanations such as ecological and paleoclimatic factors have received little attention. Here, we analyzed the role of several of these factors to describe the phylogeographic patterns of the desert mistletoe, Phoradendron californicum.

Methods: Using noncoding chloroplast regions, we assess the marginal probability of 19 a priori hypotheses related to geological and ecological factors to predict the cpDNA variation in P. californicum using a Bayesian coalescent framework. Complementarily, we used the macrofossil record and niche model projections on Last Glacial Maximum climatic conditions for hosts, mistletoe, and a bird specialist to interpret phylogeographic patterns.

Key results: Genealogical reconstructions revealed five clades, which suggest a combination of cryptic divergence, long-distance seed dispersal, and isolating postdivergence events. Bayesian hypothesis test favored a series of Pliocene and Pleistocene geological events related to the formation of the Baja California Peninsula and seaways across the peninsula as the most supported explanation for this genealogical pattern. However, age estimates, niche projections, and fossil records show dynamic host-mistletoe interactions and evidence of host races, indicating that ecological and geological factors have been interacting during the formation and structuring of phylogeographic divergence.

Conclusions: Variation in cpDNA across the species range results from the interplay of vicariant events, past climatic oscillations, and more dynamic factors related to ecological processes at finer temporal and spatial scales.