Deep biogeographical history and cytonuclear discordance in the black‐tailed brush lizard ( Urosaurus nigricaudus ) of Baja California

Molecular tools help us deduce historical events such as vicariance, dispersal, gene flow and speciation. However, our inferences are inevitably linked to the nature of the characters that we use to infer history. For example, the difference in inheritance patterns of mitochondrial DNA (mtDNA) and nuclear DNA (non‐recombining maternal vs. recombining biparental inheritance) may lead us to propose different intraspecific histories. The peninsula of Baja California of north‐western Mexico, a region affected by a complex geological history involving temporary seaways, permits evaluation of differences between these character types. We sequenced 1966 bp of mtDNA to reconstruct the genealogical history of Urosaurus nigricaudus (black‐tailed brush lizard) from samples spanning the entire peninsula. The genealogy revealed several deep divergences, congruent with temporary vicariance events in the mid‐peninsular, Loreto and Cape regions, as well as a major split across the Isthmus of La Paz, possibly resulting from a late Miocene seaway. The results support an emerging picture of the historical biogeography of Baja California, which suggests that key vicariance events are older than commonly perceived. The maternal genealogy of U. nigricaudus sharply contrasts with variation in allozymes that suggests very little differentiation across mitochondrial breaks, consistent with a pattern of ongoing gene flow. We interpret this cytonuclear discordance in relation to the historical biogeography of the region. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 89–104.