Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence
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, marker bias, and dispersal abilities. The Baja California peninsula and adjacent desert regions include several biogeographic barriers that have left phylogeographic patterns in some but not all species. We found that mitochondrial DNA, single nuclear genes, and genome-wide SNP data sets show largely concordant phylogeographic patterns for four bird species along the Baja California peninsula and adjacent mainland: cactus wren, Gila woodpecker, California gnatcatcher, and LeContes thrasher. The cactus wren and LeContes thrasher show a concordant historical division at or near the Vizcaino Desert in north-central Baja California, the Gila woodpecker appears to be at an intermediate stage of divergence, and the California gnatcatcher lacks notable phylogeographic structure. None of these four species are classified taxonomically in a way that captures their evolutionary history with the exception of the LeContes thrasher. We also present mtDNA data on small samples of ten other species that span the Vizcaino Desert, with five showing no apparent division, and five species from the Sierra de la Laguna, all of which appear differentiated. Reasons for contrasting phylogeographic patterns should be explored further with genomic data to test the extent of concordant phylogeographic patterns. The evolutionary division at the Vizcaino 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 Vizcaino Desert, which contains considerable diversity, should be recognized as historically significant areas for conservation.