taking place only within the last 5 million years (Morgan and Swanberg 1985). The Colorado Plateau is drained by the Colorado River; hence, elevation changes of the Plateau have had major impacts on the directions of flow and drainage connectivity. The uplift resulted in the isolation of the Colorado Plateau as north-flowing streams from central Arizona were interrupted. Also, the uplift of the Wasatch Front, starting in the early Eocene, and the subsequent drop of the Great Basin in late Oligocene isolated the upper Colorado River fauna from that of the Great Basin along its northwestern margin (Figure 3.2).
Origins of the upper Colorado River fish fauna (including watersheds of the Green and Colorado rivers) are ancient, likely having begun in the Oligocene and Miocene in streams draining the uplifted Rocky Mountains and flowing across the Colorado Plateau to interior basins in Colorado and New Mexico (the Miocene Bidahochi Basin) or northwestern Arizona (the Miocene Hualapai Basin) (Figure 3.2) (Oakey et al. 2004). A middle section of the Colorado River, currently comprising the Little Colorado, Virgin, and White rivers, drained to the southwest, while a third section, including the Gila River, was incorporated into the drainage after the retreat of the Bouse Miocene/Early Pliocene Embayment (Minckley et al. 1986)—an embayment that, while first thought to be a marine or estuarine extension of the Gulf of California, now appears to have been a series of lakes, with perhaps the lower being saline (Dillon and Ehlig 1993; Spencer and Patchett 1997; Roskowski et al. 2007). The upper and lower Colorado River systems were joined perhaps 10.6 to 3.3 mya, following headward erosion of streams of the middle and lower Colorado watersheds and through reoccupation and reversal of flow in older channels (Figure 3.2). Prior to this time, the upper Colorado River drainages flowed into a closed basin. It was not until the Pliocene that the Colorado River reached the Gulf of California (Minckley et al. 1986; Powell 2005).
The origins of the dominant components of the mainstem Colorado fish assemblage (Colorado Pikeminnow, Ptychocheilus lucius; Humpback Chub, Gila cypha; Roundtail Chub, G. robusta; Bonytail Chub, G. elegans; Speckled Dace, Rhinichthys osculus; Razorback Sucker, Xyrauchen texanus; Bluehead Sucker, Catostomus discobolus; and Flannelmouth Sucker, C. latipinnis) can be traced to these various geological events (Minckley et al. 1986; G. R. Smith et al. 2002). Most of the species have their closest relationships with populations in the north and west, but some also show relationships to the south. Colorado Pikeminnow, and Roundtail, Humpback, and Bonytail chubs, show relationships to the north and west, including the Sacramento-San Joaquin Basin in what is now California, but also to the Miocene Bidahochi Lake deposits to the southeast (Figure 3.2).
FIGURE 3.2. The Colorado Plateau (dark gray), Colorado River Drainage, and Great Basin (light gray), including other features mentioned in the text. The dotted line indicates the area covered by the map inset, which shows periodic connections of the Bonneville Basin with the upper Snake River. The Bonneville Basin (indicated by the light shading in the inset) reached its maximum extent during the late Pleistocene; dashed lines in the inset show boundaries of the two Utah sucker clades. Based on Minckley et al. (1986), Curry (1990), Spencer and Patchett (1997), Gross et al. (2001), Johnson (2002), Cook et al. (2006), and Desert Fishes Council (2012).
Although somewhat uncertain, Speckled Dace may have originated from populations in Tertiary Lake Idaho or ancestral Snake River drainages (Oakey et al. 2004) and thus would have relationships to the north and west. Speckled Dace are characteristic of highergradient, smaller streams and show extensive genetic structure among populations, including those in the Colorado River; populations occupying the upper, middle, and lower Colorado River form three distinct genetic groups (Oakey et al. 2004).
The Flannelmouth Sucker also shows relationships to the north and west, and the Bluehead Sucker shows relationships with forms in the Bonneville Basin to the west. Origins of the distinctive Razorback Sucker are less understood, but the divergence of the Xyrauchen lineage from that of Deltistes and Chasmistes likely occurred in the late Miocene, if not before, and suggests a relationship to the north or northwest (Miller and G. R. Smith 1981; Hoetker and Gobalet 1999).
The available evidence indicates that the Colorado River fish fauna is ancient and many of the changes in species composition predate Pleistocene events. Because of the age and action of climatic and tectonic events, faunal assembly of the main-channel Colorado River fish fauna likely occurred as a series of additions, separated in space and time, so that the modern fauna is a composite of species of different evolutionary origins and ages. However, it is also important to recognize that the post-Pleistocene history of the region is again characterized by physical changes. For instance, although the southwestern region has progressively become warmer and drier, the pattern is not one of continuous warming and drying but one of high variability in climatic patterns, including periodic severe droughts.
The impact of post-Pleistocene drought on western fishes is illustrated by work on genetic variability in Flannelmouth Sucker, one of the ancient, endemic species of the Colorado River. Genetic diversity in Flannelmouth Sucker is surprisingly limited for such an ancient species and is consistent with the hypothesis of a major, basin-wide, population crash during a known time (post-Pleistocene) of severe western drought, followed by a period of rapid repopulation growth and range expansion during a wetter period. Populations of Flannelmouth Sucker in the upper regions of the Colorado basin are the result of migration from refugia in the lower part of the system, generally within the last 10,000–11,000 years (Douglas et al. 2003).
Great Basin
The Great Basin comprises a large area of complex geology located northwest of the Colorado Plateau and including large areas of Nevada and Utah and parts of southeastern Oregon, southern Idaho, southwestern Wyoming, eastern California, and northern Mexico (Figure 3.2). As suggested by the term “Great,” the Basin makes up almost 20% of the United States and constitutes the largest inland drainage in North America (Sigler and Sigler 1987). It includes more than 150 smaller drainage basins separated by approximately 160 regularly spaced mountain ranges forming the basin and range topography (G. R. Smith 1978; Sigler and Sigler 1987; Sada and Vinyard 2002). Two large subbasins make up the Great Basin—the Bonneville Basin, occurring primarily in eastern Nevada and Utah, and the Lahontan Basin to the west, occurring mostly in Nevada and parts of eastern California. Most of the topography was formed in the last 20 million years, and many of the genera of fishes have occupied the area since the Pliocene (approximately 5 million years ago) and some since the Miocene (G. R. Smith 1981; Dowling et al. 2002; G. R. Smith et al. 2002). The fish fauna includes at least 102 species and subspecies in 15 genera of generally small-bodied forms, but the unique feature is the high level of endemism of both fishes and invertebrates (Sada and Vinyard 2002; G. R. Smith et al. 2010). At least 66% of the fish species are endemic to the Great Basin, most to specific drainages within the region (G. R. Smith 1978; Sada and Vinyard 2002). During the Pliocene and Pleistocene, repeated periods of high rainfall and changes in drainages due to volcanism resulted in a series of lakes, many quite large, in the Great Basin and created a very different environment compared to the modern-day desert—in fact, what is now Nevada was a land of abundant natural lakes (Figure 3.3). As shown by the green areas in Figure 3.3, some of the highest lake levels occurred in the early-middle Pleistocene, approximately 650,000 years ago (Reheis 1999). Two of the largest lakes were Lake Lahontan to the west and Lake Bonneville to the east. The Bonneville Salt Flats are part of the remains of Pleistocene Lake Bonneville, which is survived by the modernday Great Salt Lake and two smaller freshwater lakes, Bear and Utah, in the northeastern part of the Great Basin (Figs. 3.2 and 3.3) (Mock et al. 2006). The large Pleistocene lakes and interconnecting streams allowed aquatic organisms to colonize many of the lake basins; however, the subsequent increasing aridity during the late Pleistocene and post-Pleistocene, in part caused by the uplift of the Sierra Nevada Mountains, resulted in the isolation of the faunas, contributing to the high level of endemism and also to the frequent loss of species through extinction (Hubbs et al. 1974; Reheis 1999; G. R. Smith et al. 2002). Especially because of competition for the limited water in the now arid region, human impacts on the rate of extinction have also been particularly great (Sada and Vinyard 2002).
