Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence.

[Display omitted] • The plants and animals of the Baja Peninsula include diverse geographic patterns of evolutionary divergence. • The patterns likely stemmed from common events in earth history, such as a mid-peninsular seaway. • We compared phylogenetic analyses of multilocus sequence data to previous studies of mitochondrial and nuclear DNA. • All data sets agree that three species are concordantly differentiated at the Vizcaino Desert, and one species, the California gnatcatcher, shows no geographic differentiation. • The phylogenetic patterns of genetic divergence aid conservation by suggesting areas for reserves, and showing that some subspecies are distinct evolutionary or taxonomic units. Comparative phylogeography explores the historical congruence of co-distributed species to understand the factors that led to their current genetic and phenotypic structures. Even species that span the same biogeographic barrier can exhibit different phylogeographic structures owing to differences in effective population sizes, genetic marker bias, and dispersal abilities. The Baja California peninsula and adjacent desert regions include several biogeographic barriers, including the Vizcaíno Desert and Sierra de la Laguna (Cape District), that have left phylogeographic patterns in some but not all species. We used genome-wide SNP data to test the hypothesis that the diverse phylogeographic patterns inferred from prior studies were supported. We found that mitochondrial DNA, single nuclear gene, and genome-wide SNP data show that the cactus wren and LeConte's thrasher have a concordant historical division at or near the Vizcaíno Desert in north-central Baja California, the Gila woodpecker is at an intermediate stage of divergence, and the California gnatcatcher lacks phylogeographic structure. None of these four species are classified taxonomically in a way that captures their evolutionary history with the exception of the LeConte's thrasher. We also analyzed mtDNA data on samples of nine other species that span the Vizcaíno Desert, with four showing no apparent division, and six additional species from the Sierra de la Laguna, all but one of which are differentiated. Reasons for contrasting phylogeographic patterns among these species should be explored further with genomic data to test the extent of concordant phylogeographic patterns. The evolutionary division at the Vizcaíno desert is well known in other vertebrate species, and our study further corroborates the extent, profound effect, and importance of this biogeographic boundary. The areas north and south of the Vizcaíno Desert, which contains considerable diversity, should be recognized as historically significant areas for conservation. [ABSTRACT FROM AUTHOR]