The avifauna of California emerged as the result of colonization from a number of different biogeographic areas and increased in diversity during the Paleogene. Upwelling during the Miocene was likely important in the radiation of the Alcidae and other shorebirds. Pleistocene glaciations and climatic changes had effects on the phylogeographic pattern in many species, including Aves. Worldwide, it is estimated that there were twenty-one thousand bird species at the beginning of the Pleistocene, but by the end of the Pleistocene, only ten thousand species remained. Boreal birds with large distributions in glaciated North America diverged in the Pleistocene due to divergent selection in different ecological habitats, many of which show evidence of refuge in Northern California. However, birds with large ranges in sub-boreal or tropical environments diverged prior to the Pleistocene. It is unclear if Pleistocene glaciation cycles resulted in speciation rates higher than background rates. Species that show evidence of retreat to southern refugia during glaciation events include Agelaius phoeniceus and others. Refugial populations of Chamaea fasciata and others were present in the Transverse Ranges region. Habitat and climatic differences correspond to divergence of Pica nuttalli and P. hudsonia, among other species, between California and central Mexico. Migratory species generally have more uniform genetic distributions than nonmigratory species, but their genetic structure is affected by breeding range.
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