Three previous studies used non-quantitative methods to estimate the proportion of G. sila habitat lost to development. They estimated that between 80–94% of habitat had been lost [ 10 , 26 , 53 ]. Based on our analysis of habitat lost to agriculture, development, and fragmentation (68% of habitat), discovery of apparent vegetation and climate-mediated extirpations and range contraction, the large proportion of sites where G. sila have not been seen for decades, and other sources of unquantified habitat loss and degradation, we conclude that these previous estimates may reasonably bracket the proportion of habitat loss and range contraction experienced by the species. Other unquantified sources of habitat loss and degradation include off-road vehicle use, petrochemical extraction, solar infrastructure, aerial application of insecticides, and atmospheric nitrogen deposition [ 24 , 52 ].

The high proportion (49%) of historical occurrence locations on intact habitat where G. sila have not been documented for over two decades is of great concern. Many of these sites may have suffered extirpation as a result invasion by exotic annual grasses and forbs. Over 25 years ago, Germano and Williams [ 26 ] identified a range-wide status survey as a top priority for G. sila recovery, noting that “no status survey has ever been conducted, even though the species was first federally listed in 1967.” We echo the importance of conducting this type of range-wide survey. A status survey is necessary to fully evaluate the conservation status and potential future recovery of the species. Resurveying old occurrence locations may also aid in resolving uncertainty in how species will respond to climate change ( S1 Text ). Few reports from previous surveys have recorded where G. sila were not detected (but see [ 47 ]). Documenting such information would enable ecologists to shift from a modeling framework based on presence data only to a more robust occupancy modeling framework and improve the capacity for species management and conservation.

Where habitat remains undeveloped, invasion of exotic annual grasses and forbs appears to be responsible for peripheral range contraction from the mesic margins of the distribution of G. sila. Before European colonization of California, native habitat provided areas of relatively bare soil [ 21 ], important for lizard locomotion while hunting and evading predators, and for basking [ 13 ]. Today, widespread invasion by exotic annual grasses and forbs has resulted in dense thatch that precludes these behaviors, and leads to demographic decline [ 10 , 11 ], particularly in peripheral portions of the species range where higher precipitation adds to herbaceous productivity. Though many invasive grasses and forbs that affect G. sila were first introduced to California more than a century ago, the patterns we observe in occurrence data suggest that vegetation-mediated range contraction of G. sila may be still unfolding ( Fig 4 ). The full effects of biological invasions are mediated by stochastic processes and can take millennia to unfold [ 50 , 51 ]. Anthropogenic nitrogen deposition has likely exacerbated the impacts of exotic grasses and forbs on SJD endemic species, and its impacts are worthy of further investigation [ 52 ]. Grazing by livestock and native kangaroo rats can reduce thatch and mitigate the impact of invasive grasses and forbs [ 35 , 48 ]; however, even in areas under active management (e.g., vegetation restoration, grazing to thin excess herbaceous growth, etc.), such as at Allensworth Ecological Reserve, Pleasant Valley Ecological Reserve, and Pixley National Wildlife Refuge, G. sila populations have declined precipitously since the 1990s [ 24 ].

Despite the presence of dozens of threatened and endangered species, loss of natural habitat continues in the SJD. Over the past half century, habitat destruction in the SJD has slowed but it has not halted or reversed ( Fig 3 ). The estimated amount of G. sila habitat lost since the species became protected is greater than the total amount of habitat currently protected through public ownership and conservation easement. Unmitigated habitat loss to agricultural and other land conversion continues on large parcels of habitat, including areas with documented G. sila occurrence, areas adjacent to protected lands, and areas that formerly served as corridors connecting large patches of habitat ( S5 Table ). These trends appear to be generalizable to other upland endangered species of the SJD.

Habitat protection, restoration, and reintroduction priorities

In the midst of the downward trend in intact habitat in the SJD, a trend toward retirement of marginal farmland has also emerged [49]. Much farmland in the western SJD is of marginal quality and suffers from salinization due to irrigation of saline soils with low permeability clay layers [54], making irrigated agriculture unsustainable [55]. Climate change in the SJD is also contributing to reduced water availability and increased evaporation [56–58]. The trend toward fallowing and retirement of farmland is projected to continue as climate change exacerbates drought stress and basins come into compliance with California’s Sustainable Groundwater Management Act [9].

We identified 610 km2 of farmland with strong potential for habitat restoration. These lands were continuously fallow for three years of the California megadrought (2013–2015) and would contribute to sufficiently large patches of habitat for a high probability of G. sila population persistence. Because the drivers of which lands are retired in response to reduced water availability are likely to be constant over time (i.e. farmland soil quality, water rights) we believe that these lands can serve as a preview of some of the areas that are likely to be retired over the coming decades. With more than 2,000 km2 of SJD farmland projected to be retired in the next 30 years as basins adapt to reduced water availability, habitat restoration could represent an important contribution toward the recovery of dozens of threatened and endangered species. Restoration is attractive because it potentially reverses the trend of habitat loss as opposed to merely slowing decline. Nevertheless intact habitat tends to be superior to restored habitat [59]. Efforts toward restoration should not supplant, but rather should supplement traditional methods of habitat protection and management. Both approaches may be used in concert to conserve a diverse portfolio of sufficiently large patches of habitat.

The prospect of restoring land that is no longer cost-effective for agriculture may represent an efficient means of habitat conservation; however, more knowledge and experimentation is needed to understand the timeline and parameters that influence habitat suitability for threatened and endangered species on such lands [60]. Currently, only one study has evaluated restoration on retired farmland in the SJD [61]. The study evaluated upland restoration treatments ranging from the “do nothing approach” of simply letting natural processes carry out on their own, to more intensive treatments, including various combinations of sowing native seeds, burning, weed management, irrigation, and microtopographic grading. Among other findings, Laymon et al. [61] found the number of years that sites were fallow was positively correlated with native plant cover. Elsewhere, we have observed that G. sila and other endangered species have recolonized dryland farmland that has been retired for decades in the absence of any restoration interventions (S6 Table). Given enough time, and proper conditions, simply retiring land may be sufficient for some aspects of habitat recovery. Low-cost, high-reward interventions that could expedite recovery might include translocating native ecosystem engineers such as Heermann’s kangaroo rats (Dipodomys heermanni), re-establishing native shrubs, microtopographic grading, and a combination of targeted grazing by livestock and burning to control weeds [11,35,48,61]. In addition to treatments mentioned above, translocations of key vertebrate and invertebrate species and inoculation of soil microorganism may be beneficial when local sources are not present [62]. Restoration efforts should serve as experiments for evaluating the context dependent efficacy of various treatments. If success can be demonstrated, restoration could serve in tandem with protection of undisturbed lands as an effective strategy for recovery of threatened and endangered species.

We encourage consideration of the following factors in prioritizing land for protection and restoration. First, sandy and alkaline soils appear to be ideal for conservation in the SJD; they support less growth by exotic grasses and forbs, they are associated with occurrence of G. sila on intact habitat (S2 Fig), and they have higher native plant cover following habitat restoration on farmland [61]. Second, potential linkages between existing patches of protected habitat may be especially valuable and should be prioritized [63]. Our maps reveal several such potential linkages including both on unprotected intact habitat and on farmland with strong potential for retirement and restoration. Third, many of the areas with high potential for permanent retirement encompass or are proximate to historical occurrence records of G. sila, providing additional evidence that these areas once served as habitat and have potential to again serve as habitat. These include areas that are not adjacent to intact habitat and where translocation may be necessary to re-establish populations. Finally, a prudent strategy for conserving endangered species in the face of uncertainty is to maintain a diverse portfolio of genetic lineages on climatically and environmentally differentiated habitats [64]. Recent analysis of G. sila genomic and mitochondrial datasets [31] identify six regional groups that generally align with recovery areas designated by the U.S. Fish and Wildlife Service [24]. Conservationist should prioritize habitat protection for the clades that are underrepresented by current habitat protections.