Paleoendemics or relictual taxa may have fossil records far beyond their contemporary ranges, like ironwood (Lyonothamnus), found in western Nevada fossil beds but now confined to the Channel Islands. They often occur in discontinuous populations, like the coastal redwood (Sequoia sempervirens) and giant sequoia (Sequoiadendron giganteum), thought to be remnants of once-broader distributions. Usually their habitats are more benign than the surroundings, with higher-than-average summer rainfall and/or mild summer temperatures. Paleoendemics are also classically diagnosed by lacking close relatives nearby, since they represent old and shrinking lineages. The closest relatives of many Californian paleoendemics are found in eastern North America or eastern Asia (Stebbins and Major 1965; Raven and Axelrod 1978). By contrast, neoendemics belong to lineages undergoing recent speciation, so they may occur in complexes of closely related and adjacent species and may be poorly differentiated in morphology, genetics, and/or reproductive compatibility. Examples are discussed in Chapters 3 and 4.
The concepts of paleoendemism and neoendemism have also been applied to edaphic (soil) endemism. Paleoendemism is illustrated by species such as leather oak (Quercus durata), which is confined to serpentine soils but scattered across California and is believed to have once occurred widely on other soils but to have become restricted to serpentine through changes in the climate and/or competitive environment. Neoendemism is exemplified by species such as Layia discoidea, which appears to have arisen recently from a nonserpentine ancestor and to have been restricted to serpentine ever since it evolved (Baldwin 2005).
The distinction is not absolute, of course. Although Lyonothamnus is paleoendemic as a genus, its extant representative, L. floribundus, with its two distinctive subspecies, probably evolved recently on the Channel Islands (Erwin and Schorn 2000). The Streptanthus glandulosus complex appears to consist of a widespread species that became fragmented (similar to a paleoendemic), but some of its members have speciated recently as a result of their restriction to serpentine soil (Mayer et al. 1998). Although the prefixes paleo- and neo- imply differences in age, it should not be assumed that paleoendemic lineages are older unless (as is seldom true) this is actually tested.
It is usually assumed that neoendemism accounts for most of the wealth of endemism in California. It is certainly true that most of the studies of plant endemism in the state have focused on the evolutionary processes giving rise to new species in the region. As a background to the following chapters, the rest of this section briefly reviews modes of speciation by which new endemics evolve. The fundamental challenge is to understand how a single lineage can give rise to two (or more) descendant lineages that remain on separate evolutionary pathways rather than lose their integrity through gene flow. Geographic barriers, natural selection, hybridization, chromosomal rearrangements, and genetic architecture play roles that have been studied and debated for decades.
Geographic Speciation
One basic distinction is between geographic and ecological speciation, where the former implies a strong role for external barriers to gene flow as opposed to natural selection. In the classic model of gradual allopatric divergence, an ancestral lineage becomes subdivided by a new mountain range, water body, or similar obstacle. Sequential fragmentation may result in complexes of species with parallel patterns of genetic distance, morphological variation, and variable interfertility. Relatives that co-occur tend to have diverged longer ago than relatives that do not, suggesting that isolation promoted their initial divergence (Baldwin 2006). This is a classic and uncontroversial mode of speciation. It has been studied using the methods of biogeography, where the distributions of closely related taxa are interpreted in light of geologic and climatic events, and more recently using phylogeography, where the genetic patterns within lineages are similarly correlated to historical earth surface events. Biogeographic and phylogeographic evidence suggest that nearly all North American mountain chains are “suture zones,” that is, places where plant and animal lineages have diverged and sometimes come into secondary contact (Swenson and Howard 2007).
Ecological Speciation
Natural selection in response to new ecological opportunities is central to ecological speciation. The most spectacular examples are the adaptive radiations that sometimes occur on newly formed islands or in islandlike habitats (e.g., Price 2008). Speciation into new niches also takes place in habitats already full of species, but formidable obstacles make its success unlikely (Levin 2004). Ecological speciation begins with a small lineage colonizing a habitat in which it is ill adapted. It is more likely to go extinct than to continue evolving because of its small population size, its low genetic variability, and the reduction in its potential population growth implied by the existence of strong selective pressures. Also standing in the way of successful adaptation are gene flow from populations in the ancestral habitat and correlations between adaptive and nonadaptive genetic traits. Even if the fledgling species becomes well adapted to its new environment, it risks being genetically swamped by its progenitor species until intrinsic reproductive isolation evolves, which may take longer than adaptation to the habitat. Hybrid origins and allopolyploidy help overcome these obstacles by creating immediate reproductive barriers between a newly adapted species and its ancestors; however, the new species may be ecologically outcompeted by its relatives unless it inhabits a novel niche (Levin 2004). Other pathways to reproductive isolation include strong selection against hybrids (Kay et al. 2011), selection that incidentally favors differences in reproductive traits (e.g., flowering phenology, floral morphology), and linkage or epistatic interactions between genes involved in adaptation and genes that confer reproductive isolation (Wu et al. 2007).
Progenitor-Derivative Speciation
Another basic distinction is whether speciation results in sister taxa with roughly equal initial population sizes, geographic ranges, and genetic diversity, as in classic gradual allopatric divergence, or whether it involves a small population budding off within the range of a widely distributed species. The latter case, called peripheral isolate formation or progenitor-derivative speciation, leads to a localized neoendemic species that is phylogenetically embedded in its ancestral species. The ancestor then becomes paraphyletic; that is, it does not include all descendants of a single common ancestor. Progenitor-derivative speciation appears common in plants (Grant 1981; Gottlieb 2003; Baldwin 2006). It is related to the classic idea of “catastrophic speciation,” in which a sudden event causes a population decline in a widespread species, allowing a random chromosomal arrangement to become rapidly fixed in a small population that evolves into the derivative species. Chromosomal alterations, novel habitats, breeding system changes, and adaptive morphological differences may contribute to reproductive isolation between progenitor and derivative species. Changes appear to be moderate and to involve a small number of genes, and overall genetic similarity between progenitor and descendant remains high (Gottlieb 2003).
Hybrid and Polyploid Speciation
The origin of new species through hybridization and/or changes in chromosome number is sometimes detected in animals but is central to evolution in plants. In his classic Plant Speciation (1981), Grant argued that patterns of relatedness among plant lineages are so often network-like, due to both modern and ancient hybridization events, that the standard view of evolution as a branching “tree of life” may not apply. Hybridization generates adaptive potential because it increases genome size and allows various duplicate genes to be turned on or off in hybrid progeny. Hybridization between species with different chromosome numbers or structures initially produces progeny of low fertility because of chromosomal incompatibility, but chromosomal doubling or other rearrangements may restore fertility, in addition to causing reproductive isolation between hybrid and parental lineages. The resulting allopolyploid hybrids are thought to be particularly capable of rapid evolution because they have the full chromosomal complement of both parents. Hybridization between parental species with the