There is much excellent phylogenetic work on California plant species, but the molecular tools used thus far are generally more useful at discerning evolutionary relationships that occurred prior to the Pleistocene. Some species were survivors of disjunctions among previously widely distributed taxa and some arrived via dispersal. There is good evidence that many California plant clades are the result of Miocene migrations across Beringia. Although likely originating from the Old World, several California genera have evolutionary divergence centered in western North America and illustrate the phylogeography of flowering plants of California. Diversification on complex substrates during fluctuating climates has resulted in high levels of endemism throughout the state, but particularly in the Klamath-Siskiyou and Coast Ranges. Evolutionary processes within California’s many endemic species undoubtedly included allopolyploidy, autopolyploidy, and apomixis. Secondary contact resulting in hybridization—as a result of colonization from multiple refugia—has led to interesting genetic patterns of reticulation in many taxa. Much phylogeographic work remains to be conducted on the flora of California, particularly those species that occur in the Klamath-Siskiyou region and those with distributions in the Transverse Ranges and southern Sierra Nevada. Endemics with the most restricted distributions are present in the central Coast Ranges, the Sierra Nevada, and the San Bernardino Range, with the youngest neoendemics identified from the Desert and Great Basin.
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