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The San Joaquin Desert of California: Ecologically Misunderstood and Overlooked
Abstract and Figures
The vegetation community of the San Joaquin Valley of California has been formally classified as a perennial grassland based largely on assumptions of past climax state. However, historical records suggest that the region might be more accurately classified as a desert. The distinction is important in determining the appropriate management strategies for this ecosystem, particularly for the many rare and endemic taxa that reside there. Abiotic and biotic factors—including low precipitation, arid soils, and desert-adapted plants and vertebrate—are consistent with conditions typical of desert areas. We examined the distributions of these factors to define the extent of the San Joaquin Desert. We conclude that the San Joaquin Desert historically encompassed 28,493 km2 including the western and southern two thirds of the San Joaquin Valley, and the Carrizo Plain and Cuyama Valley to the southwest. However, this ecosystem has been reduced by up to 59% from agricultural, industrial, and urban activities. The conservation of the unique biodiversity of this region is dependent upon this ecosystem being appropriately managed as a desert and not as a perennial or annual grassland.
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... The decreased soil temperature can also increase soil moisture available to the established deeper-rooted perennial natives, increasing productivity . The RDM can be thick and impenetrable making it difficult for some small vertebrate species (some federally listed as threatened or endangered) to move on the landscape, increasing incidence of predation, and decreasing survival (Germano et al. 2011). ...
... In such cases it may take decades for the native perennial vegetation to recolonize the site and if the cycle of fire continues then the perennials will never reestablish (Brooks et al. 2004 , Germano et al. 2011. This system was highly productive benefitting from warm temperatures, abundant sunshine, and nutrient-rich alluvial soils. ...
... By contrast, sites heavily invaded by grasses form dense blankets of RDM ( Fig. 3C) in years when the rainfall quantity and timing is conducive to grasses. In such years the abundant RDM limits the mobility of these animals, leaving them more susceptible to predation and unable to forage as effectively (Germano et al. 2011). Large mature shrubs produce an abundance of viable seeds during the growing season (September-January) but relatively few seeds germinate in most years. ...
... The San Joaquin Desert region (Germano et al. 2011) has been a focal area for photovoltaic solar energy development due to an abundance of mostly flat terrain, high insolation rates, and relatively low land prices (Butterfield et al. 2013;Pearce et al. 2016;Hoffacker et al. 2017; Phillips and Cypher 2019). One of the densest concentrations of rare species in the United States also occurs in this region (USFWS 1998;Germano et al. 2011) creating the potential for significant conflict between development and conservation (Phillips and Cypher 2019). ...
... The San Joaquin Desert region (Germano et al. 2011) has been a focal area for photovoltaic solar energy development due to an abundance of mostly flat terrain, high insolation rates, and relatively low land prices (Butterfield et al. 2013;Pearce et al. 2016;Hoffacker et al. 2017; Phillips and Cypher 2019). One of the densest concentrations of rare species in the United States also occurs in this region (USFWS 1998;Germano et al. 2011) creating the potential for significant conflict between development and conservation (Phillips and Cypher 2019). Despite this potential, several utility-scale solar plants have been constructed in the region and more are planned (e.g., Kern County Planning Department 2020). ...
... The San Joaquin Desert includes the arid western and southern portions of the San Joaquin Valley, the Carrizo Plain, and some smaller valleys along the eastern edge of the Coast Ranges (Fig. 1). Geographic, climatic, abiotic, and biotic attributes of this region are detailed in Germano et al. (2011). As stated previously, large portions of this region are highly suitable for solar energy development. ...
Photovoltaic solar power generating facilities are proliferating rapidly in California and elsewhere. While this trend is welcomed for many reasons (e.g., reducing greenhouse gas emissions), these facilities also can have profound environmental impacts, particularly to local species populations. These impacts become more significant when species of conservation concern are affected. In the San Joaquin Desert region in central California, a number of conservation measures have been routinely implemented on solar facilities, and these measures have facilitated continued use of the facilities by a number of species of conservation concern. Some of the more significant measures include permeable security fences, vegetation management, movement corridors, avoiding critical features such as dens and burrows, and vehicle speed limits. Detailed studies have been conducted on San Joaquin kit foxes (Vulpes macrotis mutica) using solar facilities in the San Joaquin Desert. Demographic and ecological attributes of foxes are similar between foxes using the facilities and foxes on nearby reference sites, and values for foxes on solar sites are within the ranges of values for foxes reported from sites within core population areas. Facilitated by the conservation measures, kit foxes are using at least six facilities in the San Joaquin Desert as are a variety of other species of conservation concern. This successful model also potentially could be adapted to other ecosystems and applied to facilities in regions outside of the San Joaquin Desert, such as the Mojave Desert. Determining whether species in other regions can use photovoltaic solar facilities and identifying the most efficacious conservation measures will require time and testing, and these efforts would benefit from collaborative efforts among landowners, solar developers, natural resources agencies, researchers, and others. The San Joaquin Desert facilities and a recent demonstration facility in the Mojave Desert provide strong evidence that solar facilities can be constructed and operated in a manner that also accommodates continued use of the facilities by some species of conservation concern.
... Monolopia congdonii is a federally-listed endangered plant endemic to the San Joaquin Desert (sensuGermano et al. 2011) in Central California. It is primarily threatened by habitat loss due to land-use changes to agriculture, urban development, and oil and gas development(USFWS 1998). ...
San Joaquin wooly-threads (Monolopia congdonii; Asteraceae) is a federally-listed, endangered annual plant species from the desert areas of the San Joaquin Valley. Its limited range puts it at risk of extinction if the climate changes in such a way as to hinder its growth and reproduction. The primary aims of the study were to 1) determine how long-lived the seeds of the M. congdonii are, a key determinant of survival of desert annual plant populations through long droughts and 2) determine how severely hotter, drier conditions impact the ability of emerged plants to grow and reproduce. Secondarily, I aimed to test two hypotheses 1) is seed longevity within the genus Monolopia correlated with habitat aridity? 2) do species’ geographic range limits represent their climatic tolerances? In testing the viability of seeds of Monolopia species collected from herbarium specimens and old field collections, I did not find evidence for the predicted pattern of seed longevity. Though, idiosyncrasies in the data suggest possible issues with the longevity of M. congdonii seeds that are collected prematurely and warrant further investigation to develop best practices for seed collections of this species. To test the climatic tolerance of M. congdonii and the relationship between geographic range and climatic tolerance, I grew several desert annual species under three manipulated water treatments. And while, M. congdonii failed to germinate, the other species showed variable tolerance for the drought treatments but this variability was seemingly unrelated to the species’ geographic range. Importantly, Monolopia lanceolata, a close relative of M. congdonii did not show exceptional vulnerability to the drought-stress conditions relative to other co-occuring species. Taken together, the results of this study enable better informed population viability analyses with the end goal of allowing recovery efforts to succeed.
... The San Joaquin Valley of California has been described as a desert based on rainfall and other factors (Germano et al. 2011). Over the past 4 years the San Joaquin Valley has experienced a severe drought due to changes in the climate. ...
... The San Joaquin kit fox (Vulpes macrotis mutica) is a small xeric-adapted canid endemic to arid scrublands and grasslands in the San Joaquin Desert of California, United States [1,2]. The San Joaquin kit fox is listed as Endangered under the U.S. Endangered Species Act and as Threatened under the California Endangered Species Act, primarily due to profound loss and degradation of natural habitat throughout its range [3]. ...
A population of endangered San Joaquin kit foxes inhabits the urban environment in the city of Bakersfield, California, United States. This population is considered important for the conservation and recovery of this species. In this novel environment, kit foxes encounter a novel competitor, that being non-native red foxes. We examined exploitative and interference competition between these two species. Based on scat analysis, both species consumed similar foods and dietary overlap was high. Red foxes also were found to usurp kit fox dens. Direct mortality to kit foxes from red foxes appears to be rare. Kit foxes and red foxes also appear to overlap spatially, although we found evidence of temporal partitioning of shared space. Based on binary logistic regression modeling, habitat attributes in grid cells used by the two species generally were similar, consistent with the spatial overlap. However, differences in specific attributes indicated that kit foxes are more likely to use areas with smaller open spaces and more human activity compared to red foxes. Competition from red foxes may be mitigated by several factors. Critical resources such as food and dens may be sufficiently abundant such that they are not a limiting factor. Some degree of spatial segregation and temporal partitioning of shared space may reduce interference competition. These factors may facilitate coexistence, and consequently, red foxes do not currently appear to constitute a significant competitive risk to this important population of endangered San Joaquin kit foxes.
... The San Joaquin kit fox (Vulpes macrotis mutica; SJKF) is endemic to the San Joaquin Desert region in central California, USA (U.S. Fish and Wildlife Service [USFWS] 1998; Germano et al. 2011). This small canid (ca. ...
The San Joaquin kit fox (Vulpes macrotis mutica; SJKF) is federally endangered due to profound habitat loss. A population of SJKF occurs in the urban environment in the city of Bakersfield, California, and may be important for SJKF conservation. We conducted a systematic survey using automated camera stations and occupancy analysis to identify suitable habitat for SJKF in Bakersfield and to estimate a conceptual carrying capacity in the urban environment. We identified high, medium, and low suitability habitat totaling 121 km², 196 km², and 40 km², respectively. Based on a mean urban kit fox home range size of 0.78 km² and an assumption of two adults in high suitability home ranges and one adult in medium suitability ranges, we estimated the adult carrying capacity in Bakersfield to be 561 foxes. This estimate seems plausible as the number of adult SJKF in Bakersfield was estimated to be 381 in 2015, and the number of foxes already had been reduced by a sarcoptic mange epidemic that began two years earlier. A carrying capacity of 561 adults would increase the estimated range-wide carrying capacity by as much as 38%. Adult density estimates derived for the urban SJKF population based on the carrying capacity (1.57/km²) and home range size (2.56/km²) were higher than estimates for foxes in natural habitats. The urban SJKF population in Bakersfield is substantial and therefore could contribute significantly to conservation and recovery efforts for SJKF. Given our results, a potential conservation strategy may be to encourage or even establish additional urban SJKF populations.
... In coastal areas, much of this decline reflects habitat conversion from alluvial sage and chaparral scrub to commercial and residential development (Richmond et al. 2016). Inland in California's San Joaquin Desert region (Germano et al. 2011), conversion of native saltbush (Atriplex) and jointfir (Ephedra) scrub to irrigated agriculture has resulted in the loss of ~810,000 hectares of native A. e. occidentalis habitat since 1945 (Butterfield et al. 2021). As the distribution of A. elegans across its range becomes ever more reduced, accurate delineation of lineage diversity within the species remains a critically important task to inform conservation planning (O'Brien and Mayr 1991;Phillimore and Owens 2006 examples), reference genomes produced by the project can serve as important tools for California conservation planners, now and in the future. ...
The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California’s coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.
... Many organisms are threatened by the projected increase in global temperatures. As ectotherms, reptiles will be disproportionately threatened because their body temperatures are dependent on the temperature of their environment (Aragón et al. 2010 (Germano et al. 2011), where already high temperatures are becoming even more extreme (Ivey et al. 2020). Adult G. sila are primarily only active for a few short months (late April through mid-July) (Montanucci 1965, Germano & Williams 2005, during which time they experience high environmental temperatures (Ivey et al. 2020). ...
Global climate change is already contributing to the extirpation of numerous species worldwide, and sensitive species will continue to face challenges associated with rising temperatures throughout this century and beyond. It is especially important to evaluate the thermal ecology of endangered ectotherm species now so that mitigation measures can be taken as early as possible. A recent study of the thermal ecology of the federally endangered Blunt-Nosed Leopard Lizard (Gambelia sila) suggested that they face major activity restrictions due to thermal constraints in their desert habitat, but that large shade-providing shrubs act as thermal buffers to allow them to maintain surface activity without overheating. We replicated this study but added a population of G. sila with no access to large shrubs to facilitate comparison of the thermal ecology of G. sila in shrubless and shrubbed populations. We found that G. sila without access to shrubs spent more time sheltering inside rodent burrows than lizards with access to shrubs, especially during the hot summer months. Lizards from a shrubbed population had higher midday body temperatures and therefore poorer thermoregulatory accuracy than G. sila from a shrubless population, suggesting that greater surface activity may represent a thermoregulatory tradeoff for G. sila. Lizards at both sites are currently constrained from using open, sunny microhabitats for much of the day during their short active seasons, and our projections suggest that climate change will exacerbate these restrictions and force G. sila to use rodent burrows for shelter even more than they do now, especially at sites without access to shrubs. The continued management of shrubs and of burrowing rodents at G. sila sites is therefore essential to the survival of this endangered species.
Climate change profoundly influences plants and animals in all ecosystems including drylands such as semi-arid and arid scrublands and grasslands. At the peak of an extended megadrought in the Southwestern USA, the microclimatic refuges provided by foundation plant species and through associated vegetation were examined. Shrubs and open interstitial spaces without a canopy but with annual plants were instrumented in 2016 and the wet season of 2017 in the central drylands of California. In both years and all seasons tested, vegetation significantly mediated fine-scale near-surface air temperature and relative soil moisture content—defined here as microclimate. The foundation species with other vegetation provided the most significant thermal refuge potential capacity for other plants and animals, but there was variation by growing season. Soil moisture content was frequently increased by the direct canopy effects of shrubs. This evidence suggests that the climate many plants and animals experience, even during an extended megadrought, is mediated by the local plants in highly impacted drylands with anthropogenic disturbance and significant water-induced challenges. Foundation species such as shrubs in drylands function as a potent starting point in examining the ecological relevance of climate at scales germane to many species locally. An ecological framework for climate resilience using shrubs will improve conservation and restoration planning in drylands.
Seeds and seed banks are fundamental components of plant community theory and experimental design in desert ecosystems. Here, we made two simple observations from previous research that used seed sowing as a first step and proposed a simple workflow comprised of 5 steps to facilitate more replicable science and control for potential confounding effects of density that can be introduced between seeds and seedlings. The first observation was that choice of seeding density was relatively arbitrary and based primarily on convenience, i.e. 10 seeds per pot was common in the seeding literature. Second, reporting of the key components needed to calculate seed density in desert experiments, wherein the primary focus was not density, was sparse and limited reproducibility and contrasts between studies for the same species. The 5 steps proposed to resolve these challenges focussed on data-checking in different categories of resources from texts to bibliometrics resources that index peer-reviewed publications and datasets archived in established data repositories. The implications of adopting this process include compiling and providing evidence justifies the choice of a reasonable and representative density for most species with an arid system in a given study and this improves replication science and higher levels of consistency in experimental design. This process will also improve the reporting in the literature that can enable novel scientific syntheses for arid ecosystems.
This chapter presents some basic concepts about grassland fire, explores the role of fire in determining where grasslands occur, and examines the impact of fire on species composition. It also illustrates how vegetation and physical site factors interact and influence fire regimes, and describes the ways in which fire can be used as a management and restoration tool. The chapter focuses primarily on California annual grasslands, which occur within the Mediterranean climate zone.
This chapter examines competitive interactions in California grasslands, first presenting the major components of grassland communities, including descriptions of their phenology and growth strategies. It then describes how various life-history characteristics affect growth and survival and the interactions between species. Finally, the chapter considers how management strategies can be used to alter competitive interactions to favor native species, including grazing regimes and seed addition.
The deserts of North America are distributed over northern Mexico and the western United States between about 23° and 45° north latitude [Fig. 1]. They owe their existence to a combination of causes. The orographic [rain-shadow] effect is primarily responsible for the aridity of the Chihuahuan Desert. In the Great Basin, there is a winter maximum in rainfall. In the Chihuahuan Desert and the Sonoran Desert, the rainfall maximum comes in summer.
California's southern San Joaquin Valley, as with much of western North America, has been invaded by exotic plant species during the past 100-200 years. The herbaceous cover of these introduced grasses and forbs often creates an impenetrable thicket for small ground-dwelling vertebrates. Contrary to some earlier descriptions of upland habitat of the southern and western San Joaquin Valley as perennial grasslands, recent evidence suggests that most of this area was a desert vegetated by saltbush scrub with sparse cover of native annual grasses and forbs. Many of the small vertebrates that evolved in these habitats, some of which are listed as threatened or endangered, are desert-adapted. These species evolved in sparsely vegetated habitats and rely on open ground to forage and avoid predation. Preliminary research indicates that populations of giant kangaroo rats (Dipodomys ingens), San Joaquin kangaroo rats (D. nitratoides), San Joaquin antelope squirrels (Ammospermophilus nelsoni), and blunt-nosed leopard lizards (Gambelia sila), all listed as threatened or endangered, are affected negatively by thick herbaceous cover. This cover also may adversely affect several listed plant species. Removing anthropogenic disturbances does not reduce or eliminate these exotic plants. Fire is effective in reducing herbaceous cover but kills native saltbush and often is costly to implement or control. Although livestock may have contributed originally to habitat destruction and introduction of exotic plants, we believe that in some years, moderate to heavy grazing by livestock is the best way to decrease the dense cover created by these exotics. Recent decisions to decrease or eliminate livestock grazing on conservation lands without definitive studies of grazing in these habitats may lead to further declines of native species and possible local extinction of some listed plants and animals.
Early Spanish explorers in the late eighteenth century found springtime California covered with spectacular carpets of wildflowers from San Francisco to San Diego. Yet today, invading plant species have devastated this nearly forgotten botanical heritage. In this lively, vividly detailed work, Richard A. Minnich synthesizes a unique and wide-ranging array of sources-from the historic accounts of those early explorers to the writings of early American botanists in the nineteenth century, newspaper accounts in the twentieth century, and modern ecological theory-to give the most comprehensive historical analysis available of the dramatic transformation of California's wildflower prairies. At the same time, his groundbreaking book challenges much current thinking on the subject, critically evaluating the hypothesis that perennial bunchgrasses were once a dominant feature of California's landscape and instead arguing that wildflowers filled this role. As he examines the changes in the state's landscape over the past three centuries, Minnich brings new perspectives to topics including restoration ecology, conservation, and fire management in a book that will change our of view of native California.