Phylogeography of California: An Introduction

Phylogeography of California: An Introduction

by Kristina A. Schierenbeck

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Phylogeography of California examines the evolution of a variety of taxa—ancient and recent, native and migratory—to elucidate evolutionary events both major and minor that shaped the distribution, radiation, and speciation of the biota of California. The book also interprets evolutionary history in a geological context and reviews new and emerging phylogeographic patterns. Focusing on a region that is defined by physical and political boundaries, Kristina A. Schierenbeck provides a phylogeographic survey of California’s diverse flora and fauna according to their major organismal groups. Life history and ecological characteristics, which play prominent roles in the various outcomes for respective clades, are also considered throughout the work. Supporting scholars and researchers who study evolutionary diversification, the book analyzes research that helps assess one of the major challenges in phylogeographic studies: understanding changes in population structures shaped by geological and geographical processes. California is one of only twenty-five acknowledged biological hotspots worldwide, and the phylogeographic history of the state can be extrapolated to study other regions in western North America. Further consideration is given to implications for conservation, recommendations concerning the biogeographic provinces that roughly define the state of California, and predictions related to climate change.

Product Details

ISBN-13: 9780520278875
Publisher: University of California Press
Publication date: 08/26/2014
Edition description: First Edition
Pages: 368
Product dimensions: 5.90(w) x 9.10(h) x 1.20(d)

About the Author

Kristina A. Schierenbeck is Professor of Biological Sciences at California State University, Chico, and a passionate advocate for conservation. She teaches evolution, plant diversity, and systematics. Her research has focused on plant evolution, especially hybridization, invasive species, and rare taxa. She has authored and coauthored dozens of peer-reviewed scientific articles appearing in journals such as Proceedings of the National Academy of Sciences, Molecular Phylogenetics and Evolution, American Journal of Botany, and Molecular Ecology.

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Phylogeography of California

An Introduction

By Kristina A. Schierenbeck


Copyright © 2014 The Regents of the University of California
All rights reserved.
ISBN: 978-0-520-95924-8



What can we do with the western coast, a coast of 3,000 miles, rockbound, cheerless, uninviting, and not a harbor on it? What use have we for such a country?

Daniel Webster, 1845

The geographic province we now call California was and in some places remains every bit as rugged and inhospitable as Webster described. The geographic parameters preventing extensive European expansion before the nineteenth century are also the landscape on which the diverse flora and fauna of this region have evolved. The goal of this book is to examine and interpret the evolutionary history of the biota in California in a geologic context, as well as subsequent patterns in regional diversity that have emerged across combined phylogenies. A number of phylogeographic patterns have indeed emerged; some previously identified are expanded here in depth, and some new patterns are recognized. A survey of the phylogeography of the flora and fauna of California's diverse biota is organized by major organismal groups, and these patterns provide the context in which to ask further questions about evolutionary diversification in an area defined by both physical and political boundaries. Comparing patterns of many organisms provides the evidence needed to construct questions that are narrower than those previously posed about the colonization of taxa extant in California. Ultimately, this review provides a context for landscape-level conservation efforts throughout the biogeographic provinces that roughly define the state of California.

There are few places in the world that rival California in both topographic and biological diversity over similarly sized geographic areas. The state of California encompasses 411,015 km2 and is 1,326 km long from corner to corner (Donley et al. 1979; Kreissman 1991). Plant communities range from Mesozoic coniferous forests along the north coast with rainfall of over 2,500 mm/year to halophytic communities in Death Valley with less than 3 mm/year of rain. In the northern Coast Ranges, an additional 200 mm/year of precipitation is added in the form of fog drip (Azevedo and Morgan 1974). California contains the highest peak in the conterminous United States (Mount Whitney, 4,406 m) and the lowest elevation in North America at Death Valley (-86 m), not more than 129 km apart. Each biogeographic region is remarkably heterogeneous in terms of topography, climate, and biological and geologic history. The diversity of species occurring within the political boundary of California cannot be rivaled in North America (Table 1.1), and Conservation International has recognized California as a globally important biodiversity hotspot (Myers et al. 2000).

Biogeographic studies of California are often focused on the California Floristic Province; however, for the purposes of colonization history from the south, north, east, and west, the biogeographic boundaries that define the California Floristic Province are expanded here to include areas beyond the state's political boundaries: the Mojave Desert to the south and southeast; the western Sonoran (Colorado) Desert and northern Baja California; the Transverse and Peninsular Ranges and Channel Islands to the southwest; the Sierra Nevada and western Great Basin to the east; the Cascade and Klamath-Siskiyou Ranges to the north and northwest, including southern parts of Oregon; the Modoc Plateau to the northeast; and the Coast Ranges, Pacific Ocean, and continental shelf to the west and northwest. Because of migration patterns, marine mammals and migratory birds and fishes are included if the breeding portion of their life cycle occurs in the California area. Somewhat arbitrarily, groups not included in this monograph are molluscs, noninsect arthropods, algae, fungi, and members of the Archaea and Bacteria domains. Although there is some literature on these groups, in particular arthropods other than insects and other marine invertebrates, it was not feasible to include the entire biota. Organization within each chapter is roughly from north to south and old to young, dependent on the literature available for each clade.

The relative geologic youth of the landforms that compose much of California combined with dynamic changes to the landscape during the late Cenozoic resulted in a variety of vicariant events over space and time. Whether species were residents of western North America since the Paleozoic or Cenozoic, geologic and climatic fluctuation had dramatic effects on their ranges and population structure and resulted in survival via refugia and range changes or extinction. Life history characteristics such as dispersal ability at each life stage, generation time, reproductive ability, and ecological characteristics such as degree of habitat specialization, competition, predation, mode of propagule dispersal, and availability of habitat or migration corridors all play an important role in the various outcomes for respective clades. The challenge of phylogeographic studies is to assess changes in population structure of once largely distributed populations or expansion from ancestral propagules into present-day population structures shaped by geologic and geographic processes.

There have been tremendous geomorphologic changes to the physical location that was to become California since the Paleozoic when the area was underwater, then moved gradually north and east and accreted to North America. These processes, combined with climatic fluctuation in the Miocene and, most recently, the Pleistocene, resulted in strong selection for both long-term residents and migrants. Species groups have radiated and resulted in incredibly diverse, ancient assemblages, as in the Klamath-Siskiyou Ranges, and the association of both paleoendemics and neoendemics along the Central Coast and in the Mojave Desert. Vicariant events such as mountain uplift and dry or arctic deserts were strong drivers of allopatric speciation throughout this process. California, because of its relative evolutionary youth, also has many examples of peripatric species, hybrid zones, and sympatric speciation. Dispersal events across very different habitats at different temporal scales have resulted in a mosaic of evolutionary scenarios.

Although California was initially explored by Europeans in the sixteenth century, there were no significant settlements until the late eighteenth century, and biological exploration of the area did not begin in earnest until the nineteenth century. Surprisingly, even Sequoia sempervirens (coastal redwood, Cupressaceae) was not formally described until 1795. The conservation of some the remoter areas of California can likely be ascribed to its relatively late European colonization. Early important contributions to the natural history of California were made by David Douglas (1799–1834), botanist; John C. Fremont (1813–90), botanist and geologist; William Brewer (1828–1910), botanist; James Cooper (1830–1902), geologist and naturalist; Willis L. Jepson (1867–1946), professor of botany at University of California, Berkeley, for over forty years; and Mary Brandegee (1844–1920), first curator of the California Academy of Sciences. A detailed account of the early, pioneering naturalists of California can be found in Beidleman's California's Frontier Naturalists (2006). Important contributions on the nature of California's diversity and the role of evolution were made by Joseph Grinnell (1877–1939), first director of the Museum of Vertebrate Zoology; Edward O. Essig (1884–1964), entomologist and founder of the entomology collection at UC Berkeley; Clinton Hart Merriam (1855–1942), mammalogist, ornithologist, and entomologist; Lincoln Constance (1909–2001), director of the University of California Herbarium; and G. Ledyard Stebbins, evolutionary botanist and founding member of the Department of Genetics at UC Davis. More contemporary contributions to understanding the evolution of the biota of California have been made by many individuals but in particular by Daniel Axelrod, Herbert Baker, Bernie LeBeouf, Robert Haller, Lloyd Ingles, Arthur Kruckeberg, Harlan Lewis, Elizabeth McClintock, Jack Major, Robert Ornduff, James Patton, Peter Raven, and Robert Stebbins. Significant groundwork in phylogeography and evolution of the biota of California since the 1980s has been laid in the laboratories of David Wake, George Roderick, Brad Shaffer, Michael Caterino, Bruce Baldwin, Brett Riddle, Victoria Sork, Arthur Shapiro, Peter Moyle, Susan Harrison, Craig Mortiz, Greg Spicer, Wayne Savage, and Robert Zink.

Phylogeography of California summarizes and synthesizes the literature of the past fifty years, beginning roughly with the insightful and pioneering work of Axelrod in the 1960s. Raven and Axelrod's pathbreaking work in 1978 provides the foundation on which California phylogeographers have built an examination of the evolution of ancient, recent, native, and some migratory taxa to elucidate the major and minor evolutionary events that shaped the distribution, radiation, and speciation of the biota of this special place. Because phylogeography is a synthetic field drawing primarily from systematics, population genetics, geography, paleontology, and ecology, integration of these fields will enable us to predict and prioritize conservation areas during a time of rapid climate change, human disturbance, and invasive species. This work is not meant to be comprehensive but to provide a summary of the published literature on the evolution and diversification of some of the biota of California. It provides trends, examples, and, it is hoped, the generation of new hypotheses.

This book begins with a brief geologic history of the formation of the landscape on which California's species have evolved, followed by an evolutionary journey from the arrival of the ancestors of California's biota through their subsequent divergence within each major taxonomic group. Although the geologic and fossil records are not the province of phylogeography per se, the formation of California throughout the Paleozoic and Mesozoic provides the context for the development of the rich geology on which the biota gradually colonized and diversified. For example, the ancient substrates of the Klamath-Siskiyou Ranges originated at different latitudes from a variety of geologic processes that resulted in the formation of Paleozoic ophiolites and Mesozoic sedimentary rocks that underlay one of the most biodiverse regions in California. Fossil records prior to the Cenozoic help provide the visualization of the gradual colonization of the region prior to the dramatic climatic and geologic events of the late Cenozoic.

The writing is directed to the informed natural historian and is appropriate for an upper-division or graduate course on phylogeography or the evolution and natural history of California. Chapters are organized variously, according to available literature and clade distributions. Readers are provided with an evolutionary perspective of the basis of regional conservation and a context for how the California biota may respond to a rapidly changing environment due to global climate change.


On the western edge of the North American Plate much of present-day California did not exist or was underwater until the Mesozoic. Plate tectonics were responsible for gradually accreting landforms to the North American Plate that became California. Land areas that were present prior to this time, which include the Mojave Desert and the Klamath Plate, have experienced dramatic changes in orientation, latitude, and climate. Following is a brief description of major contemporary landforms.

The Klamath-Siskiyou region includes the Siskiyou Mountains, Trinity Alps, Marble Mountains, Salmon Mountains, Scott Bar Mountains, and North Yollo Bolly Mountains, covering about 50,300 km2 (Miles and Gouday 1997). The current substrate is a complex array of formations from the Paleozoic and Mesozoic, primarily composed of metamorphic rocks differentiated from the generally younger geology of the Coast Ranges and the Cascade Range (Sawyer and Thornburgh 1977). This area of northwestern and north central California and adjacent Oregon contains some of the most interesting taxonomic assemblages in western North America. Although there is some evidence of glaciation about 30,000 years ago (ka), this region largely escaped Pleistocene glaciation-events, although the biota was certainly affected by climatic variability during this time. The large number of relictual plant species found in this region provides evidence that a number of high-elevation sites served as refugia (Soltis et al. 1997; Sawyer 2006).

North of the Sierra Nevada and beginning east and southeast of the Klamath-Siskiyou region is the Cascade Range, which consists of a chain of large volcanoes and dissected lava flows of early Paleogene through Holocene origin. California is home to the two southernmost volcanoes of the Cascade Range, Mount Shasta (4,319 m), a stratovolcano created by a series of eruptions over the past 600,000 to 100,000 years, and Mount Lassen (3,188 m), part of a volcanic center that began erupting 825 ka and most recently erupted during the period from 1914 to 1921. East of the Cascade Range in extreme northeastern California, the Modoc Plateau is a lava plain with an average elevation of 1,350 m, estimated to have formed from lava flows between 25 and 3 million years ago (Ma) (Schoenherr 1992; DeCourten 2008). The Modoc Plateau is also volcanically young, with activity as recent as 700 ka in the Medicine Lake area and eruptions as recently as 200 to 300 years ago (Harden 1998).

The Sierra Nevada stretches for roughly 650 km from southern Lassen County south to central Kern County, with an east-west breadth of 70–90 km (Storer and Usinger 1964; Howard 1979). Most of the base rock is a complex array of granitic plutons formed during the Mesozoic, although there are some weakly metamorphosed sedimentary and volcanic rocks of Paleozoic age that have been intruded by the granite batholiths (DeCourten 2008). Middle and upper Cenozoic rocks crop out in the northern parts of the Sierra Nevada. Geologists debate the temporal distribution of the uplift of the Sierra Nevada, but there is recent consensus that initial uplift occurred as long as 160 Ma (Cassel et al. 2009), with significant uplift from about 1,000 to 1,500 m (25 Ma) to 2,500 m (10 Ma) (Xue and Allen 2010). Pliocene uplift approximately 6–3 Ma is supported by tilted strata; however, isotope data suggest that the primary uplift occurred prior to 12 Ma (Mulch et al. 2008). The Sierra Nevada and its resident biota have been further shaped by at least nine major glaciations since the Pliocene (Gillespie and Zehfuss 2004).

The Great Valley of California lies between the Sierra Nevada and the Coast Ranges and continues about 680 km from the Klamath Mountains in the north to the Tehachapi Mountains at the southern end. It is a mostly flat plain, 60–120 km wide, undergoing deposition for as long as 100 Ma, with soils that are largely alluvial and lacustrine sediments originating from former inland seas and the nascent Sierra Nevada (Farrar and Bertoldi 1988). The Sacramento Valley occupies the northern one-third of the valley. The San Joaquin Valley occupies the southern two-thirds of the valley and comprises the San Joaquin Basin in the north and the interior-draining Tulare Basin in the south. Water flow in the valley is dispensed by the San Joaquin River in the south and the Sacramento River in the north; these rivers join approximately midway to form a delta composed of a westward series of freshwater, brackish, and salt marshes that flow into the San Francisco Bay. The San Francisco Bay estuary is one of California's most important ecological habitats, draining approximately 40 percent of the water in the state.

On the Pacific coast, south of the Klamath Range and extending to Santa Barbara County, are the Coast Ranges, a series of north-south ranges primarily of sedimentary origin that with few exceptions are less than 2,000 m in elevation (Harden 1998). Formation of the Coast Ranges is the result of a number of mechanisms. The northern ranges were formed by the movement of the North American and Pacific Plates (Atwater 1970). During the Oligocene, the Salinian terrane was located west of the present Central and Southern California coast. Beginning in the Miocene, northward movement and fragmentation of the granitic and metamorphic Salinian terrane resulted in the formation of islands that eventually became part of the Coast Ranges (Hall 2002; Kuchta and Tan 2009). Before the Pliocene, the central Coast Ranges existed as islands (Yanev 1980). About 5–3 Ma, the Santa Ynez Mountains became connected to the Gabilan and Santa Lucia Mountains via the uplift of the Temblor Range (Hall 2002). A seaway south of Monterey and present from about 8–2 Ma, was closed via continued uplift of the Coast Ranges and consequently allowed the Central Valley to fill with freshwater from the surrounding Coast Ranges and Sierra Nevada. Drainage of the Central Valley continued to occur via the Salinas and Pajaro Rivers until further uplift of the Coast Ranges about 600 ka diverted the drainage through the Carquinez Strait and into the San Francisco Bay (Sarna-Wojcicki et al. 1985).


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