The Great Basin Desert of western North America is characterized by a series of alternating islands of mountain ranges and desert basins (Fiero 1986) that formed a backdrop to a dynamic biogeographic history (Davis 2005). The glacial–interglacial cycles of the Pleistocene (Riddle 1995) and the associated rise and fall of pluvial lakes (Benson 1981), shifting climatic patterns (Atvens 1952), and floristic transitions (Reveal 1979) have caused numerous habitat alterations throughout the Great Basin Desert. More recently, anthropogenic habitat alterations (e.g., introduction of nonnative plant species, increased wildfires, and cultivation and irrigation) have also plagued the area (Hafner and Hafner 1998). These alterations have caused a significant loss of available habitat and subsequent reduction in the abundance of native fauna and flora. For example, representatives of the rodent genus Microdipodops (kangaroo mice; family Heteromyidae) have become increasingly rare members of the Great Basin Desert community (Hafner and Upham 2011).
Two species of Microdipodops are currently recognized: the dark kangaroo mouse (M. megacephalus) and the pallid kangaroo mouse (M. pallidus). Both species are sand-obligate endemics to the Great Basin Desert and, as such, are highly specialized to survive in an extreme environment (Hafner 1981). In fact, morphology within the genus is extremely conserved with only slight differences between sibling taxa (Hafner et al. 2008). Given their ecological specializations, these small nocturnal rodents likely serve as indicator species of healthy, sandy desert habitats of the Great Basin. Field observations, however, have concluded that the numbers of both M. megacephalus and M. pallidus are dwindling (Hafner 1981; Hafner and Hafner 1998; Hafner et al. 2008; Hafner and Upham 2011), as is the case for other flora and fauna distributed across the Great Basin Desert (Brussard et al. 1998). However, both Microdipodops species are listed as “Least Concern” by the International Union for Conservation of Nature (IUCN) and are not protected (Linzey and Hammerson 2008; Linzey et al. 2008). Given their decreasing numbers, this listing is outmoded and management of kangaroo mice, along with other Great Basin Desert organisms, will be necessary to help preserve this threatened ecosystem.
Microdipodops megacephalus and M. pallidus have unique habitat associations within the Great Basin Desert. Although their distributions overlap (Fig. 1), these species show differential niche specializations. Microdipodops megacephalus is primarily restricted to sandy soils with gravel overlay and found in association with sagebrush and/or rabbit brush (Hafner and Upham 2011; and references therein); whereas M. pallidus prefers greasewood and fine soils with no gravel overlay (Hafner 1981; and references therein). Ancient and current habitat alterations have led to fragmented distributions for both species such that current intraspecific ranges are disjunct (Figs. 1, 2), separated either by geological barriers (e.g., mountain ranges) or unsuitable habitat (Hafner et al. 2008; Hafner and Upham 2011).
These unique, fragmented distributions and ecological specializations have made kangaroo mice the recent subjects of several studies that used mitochondrial DNA (mtDNA) gene regions to elucidate the biogeographic history of the Great Basin Desert (Hafner et al. 2006, 2008; Hafner and Upham 2011; Light et al. 2013). These studies identified and supported four distinct mtDNA clades in M. megacephalus (the eastern, central, western, and Idaho clades; Fig. 2A) and two distinct mtDNA clades in M. pallidus (the eastern and western clades; Fig. 2B). While the identification of genetically discrete units within each species is important, additional analyses using fast-evolving nuclear markers, such as microsatellites, are necessary to verify the results of the mtDNA data. These markers also can help to estimate parameters for conservation and management of these specialized taxa; for example, estimates such as rates of gene flow and effective population sizes for Microdipodops are currently unknown. Lastly, examination of multiple markers can facilitate a better understanding of genetic lineages within a species (Avise 1994), especially as these markers may have different evolutionary histories (e.g., Yang and Kenagy 2009).
Herein, we use microsatellite markers to provide an assessment of nuclear variation within each Microdipodops species and to test the findings from previous studies which used mtDNA sequence data (Hafner et al. 2006, 2008; Hafner and Upham 2011; Light et al. 2013). We hypothesize that microsatellite markers will support discrete genetic units within each Microdipodops species and uncover the same geographic groups found in previous studies. Due to the wealth of information available regarding Microdipodops biogeography, population-level analyses are performed on microsatellite data with samples disaggregated into geographic regions identified in previous studies (Fig. 2) and results are interpreted in reference to Great Basin biogeography. These findings will help to identify evolutionarily significant units and address issues of management, conservation, and desert biogeography that can be applied to other flora and fauna of the threatened Great Basin Desert.