We report on an annotated chromosome-level genome assembly for the long-nosed leopard lizard, Gambelia wislizenii, as part of the California Conservation Genomics Project (CCGP). All 17 species of reptiles, including two turtles, seven lizards, and seven snakes targeted for reference genome sequencing by the CCGP are now complete and posted on NCBI, and this article is the third of seven CCGP lizard release papers to be published. It is also the first species of the family Crotaphytidae to have a released reference genome. Following the CCGP pipeline, the G. wislizenii genome was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data. The de novo assembly includes 69 scaffolds and has a total length of ~ 2.47 Gb, a scaffold N50 length of 380.1 Mb, and a BUSCO completeness score of 97.4% based on the tetrapod gene set. We improved the annotation of the genome using transcriptome sequencing (seven tissue types), identifying 23,279 genes, with BUSCO completeness of 98.9%. This reference genome, when combined with CCGP's on-going state-wide resequencing efforts for the three species of Gambelia in California, including the federally endangered blunt-nosed leopard lizard (Gambelia sila), and Cope's leopard lizard (Gambelia copei), will be a powerful tool enabling researchers to characterize hybridization dynamics between Gambelia species, document the remaining diversity within G. sila, and explore the genetic underpinnings of key traits that vary between the three Gambelia species, such as territoriality, sexual size dimorphism, presence versus absence of male breeding coloration, and skull morphologies.

Describing the habitat needs of endangered species is a major focus of applied conservation research. The blunt-nosed leopard lizard (Gambelia sila (Stejneger, 1890)) is a flagship endangered species endemic to the San Joaquin Valley of California, USA. Arthropods are an important component of G. sila's diet and of many other listed vertebrate species in Californian drylands. We examined the drivers of abundance, richness, and composition across the current and extirpated ranges of the blunt-nosed leopard lizard G. sila for four arthropod communities: ground-active, shrub-canopy active, open area active, and aerial. We found no evidence for lower arthropod abundance or species richness at sites from which G. sila has been extirpated. In contrast, the ground-active arthropod and beetle communities were less abundant at sites with current populations of G. sila after accounting for environmental variation. Thus, prey availability-at least at the community level and for the taxonomic groups considered-would not likely be a factor constraining future repopulation efforts for G. sila into its historical range. Beta-diversity partitioning analyses indicated that a regional approach to conservation is necessary to conserve arthropod biodiversity across the San Joaquin Valley. Increasing aridity lowered abundance and species richness at fine scales for most communities tested and was also related to spatial composition across the region. Thus, in terms of G. sila conservation and restoration, sites with the lowest current and projected future aridity should be prioritized to maximize the abundance and richness of co-occurring ground-active arthropod and beetle communities.

Aim Biodiversity conservation broadly relies on protecting suitable habitat for species of concern, and species distribution models (SDM) are a common method for classifying potential habitat suitability. However, SDMs frequently omit resource availability and are therefore missing potentially useful information for planning successful conservation areas. Here, we aim to identify regions of high prey availability, and thus high resource availability, for several listed predator species across California dryland regions. This information could be used to support more refined estimates of valuable habitat for prey species that support listed species within Central California drylands. Location California, USA. Time Period 1945-2022. Major Taxa Studied Arthropoda. Methods We used a prey list for 11 listed species found in California drylands and compiled occurrence records for those species from the Global Biodiversity Information Facility. We fit individual SDMs for all species using Bayesian additive regression trees. These individual SDMs were then stacked to identify hotspots of prey density across California. Results We found the highest observed and predicted prey richness along the Southern California coast in grassland, savanna, and urban landcover classes. Only a small region (2.9%) contained suitable habitat for more than 50% of prey species. In contrast, 60% of the study region contained suitable habitat for at least 1 prey item for more than 50% of listed predator species. Main Conclusions Observed hotspots of high prey richness and regions where predicted prey richness could support multiple listed species identify potential regions for conservation efforts. Our results also highlight how mapping prey in addition to listed species can support planning, as our stacked-SDMs identified a wide geographic extent that can support the listed species. Future research could use these stacked-SDMs to identify sites for standardised field surveys for key variables including whether predicted prey items are present but also in high abundance.

Animals can respond to extreme climates by behaviourally avoiding it or by physiologically coping with it. We understand behavioural and physiological thermoregulation, but water balance has largely been neglected. Climate change includes both global warming and changes in precipitation regimes, so improving our understanding of organismal water balance is increasingly urgent. We assessed the hydric physiology of US federally endangered blunt-nosed leopard lizards (Gambelia sila) by measuring cutaneous evaporative water loss (CEWL), plasma osmolality and body condition. Measurements were taken throughout their active season, the short period of year when these lizards can be found aboveground. Compared to a more mesic species, G. sila had low CEWL which is potentially desert-adaptive, and high plasma osmolality that could be indicative of dehydration. We hypothesized that throughout the G. sila active season, as their habitat got hotter and drier, G. sila would become more dehydrated and watertight. Instead, CEWL and plasma osmolality showed minimal change for females and non-linear change for males, which we hypothesize is connected to sex-specific reproductive behaviours and changes in food availability. We also measured thermoregulation and microhabitat use, expecting that more dehydrated lizards would have lower body temperature, poorer thermoregulatory accuracy and spend less time aboveground. However, we found no effect of CEWL, plasma osmolality or body condition on these thermal and behavioural metrics. Finally, G. sila spends considerable time belowground in burrows, and burrows may serve not only as essential thermal refugia but also hydric refugia.

Positive associations between animals and foundational shrub species are frequent in desert ecosystems for shelter, resources, refuge, and other key ecological processes. Herein, we tested the impact of the density of the shrub species Ephedra californica on the presence and habitat use of the federally endangered lizard species, Gambelia sila. To do this, we used a 3-year radio telemetry dataset and satellite-based counts of shrub density across sites at the Carrizo Plain National Monument in San Luis Obispo County, CA. The effect of shrub density on lizard presence was contrasted with previous shrub cover analyses to determine whether measures of shrub density were superior to shrub cover in predicting lizard presence. Increasing shrub density increased lizard presence. As shrub density increased, lizards were located more frequently "above ground" versus "below ground" in burrows. Male lizards had significantly larger home ranges than females, but both sexes were similarly associated with increasing shrub densities. Shrub density and shrub cover models did not significantly differ in their prediction of lizard presence. These findings suggest that both habitat measures are effective analogs and that ecologically, both cover and the density of foundation shrub species are key factors for some desert lizards.

A fundamental goal of population genetic studies is to identify historical biogeographic patterns and understand the processes that generate them. However, localized demographic events can skew population genetic inference. Assessing populations with multiple types of genetic markers, each with unique mutation rates and responses to changes in population size, can help to identify potentially confounding population-specific demographic processes. Here, we compared population structure and connectivity inferred from microsatellites and restriction site-associated DNA loci among 17 populations of an arid-specialist lizard, the desert night lizard, Xantusia vigilis, in central California to test among historical processes structuring population genetic diversity. We found that both marker types yielded generally concordant insights into population genetic structure including a major phylogenetic break maintained between two populations separated by less than 10 km, suggesting that either marker type could be used to understand generalized demographic patterns across the region for management purposes. However, we also found that the effects of demography on marker discordance could be used to elucidate population histories and distinguish among competing biogeographic hypotheses. Our results suggest that comparisons of within-population diversity across marker types provide powerful opportunities for leveraging marker discordance, particularly for understanding the creation and maintenance of contact zones among clades.

Conservation science and environmental regulation are sibling constructs of the latter half of the 20th century, part of a more general awakening to humanity's effect on the natural world in the wake of 2 world wars. Efforts to understand the evolution of biodiversity using the models of population genetics and the data derived from DNA sequencing, paired with legal and political mandates to protect biodiversity through novel laws, regulations, and conventions arose concurrently. The extremely rapid rate of development of new molecular tools to document and compare genetic identities, and the global goal of prioritizing species and habitats for protection are separate enterprises that have benefited from each other, ultimately leading to improved outcomes for each. In this article, we explore how the California Conservation Genomics Project has, and should, contribute to ongoing and future conservation implementation, and how it serves as a model for other geopolitical regions and taxon-oriented conservation efforts. One of our primary conclusions is that conservation genomics can now be applied, at scale, to inform decision-makers and identify regions and their contained species that are most resilient, and most in need of conservation interventions.

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.

—With the existence of many endangered terrestrial ectotherms now being threatened in the face of climate change, effective tools to aid in the management of their conservation are necessary. Temperature-based activity estimation (TBAE) is an automated method for predicting surface activity and microhabitat use based on the temperature of an organism and its habitat, and TBAE may be used to reduce the monitoring effort for sensitive species. However, its efficacy has not been assessed in heliothermic species. We hypothesized that heliothermy would facilitate the accurate prediction of surface activity due to the rapid changes in temperature effected by exposure to solar radiation, but that TBAE would not accurately predict microhabitat use because heliothermic lizards shuttle too frequently among microhabitats. In this study, we assessed how well ambient air temperature and lizard physical model temperature predicted surface activity and microhabitat use of a federally-listed Endangered lizard, Blunt-nosed Leopard Lizard, Gambelia sila, by comparing these variables to continuously logged active lizard body temperatures in the field. While surface activity was correctly predicted 93% of the time using either ambient or physical model temperatures, the accuracy in predicting microhabitat use only ranged from 47–72%. Finally, TBAE allowed us to predict the time of morning emergence from burrows to within approximately 11 minutes. TBAE is a promising means for remotely monitoring surface activity and morning emergence of heliotherms, however its utility in distinguishing microhabitat use in heliotherms is limited.

Telemetry has revolutionized studies in wildlife biology, ecology, physiology, and conservation. With the increased demand for telemetry, new technology has made great strides to enable long studies in harsh and remote areas on a wide variety of study species. As the climate crisis continues to impact animals, temperature-sensing telemetry has become a helpful technique for understanding the effects of climate change and how to protect wildlife from them. However, temperature-sensing telemetry and telemetry in general still pose technological challenges and accessibility issues for the researchers who use it. Currently available telemetry technology is expensive, too large and heavy for many study species, and cannot measure all variables researchers want to study. These technological improvements have especially been neglected for temperature-sensing telemetry, which may be underutilized given the current climate crisis. To understand why innovation has stalled, and where it should be directed going forward, we gathered opinions from researchers who use telemetry and from manufacturers that create and supply telemetry equipment. Our goal was to broadly describe the current technological landscape, compare it to what we envision for the future, and make suggestions for how to reach that future.

Abstract The Paris Agreement seeks to combine international efforts to keep global temperature increase to well‐below 2°C. Whilst current ambitions in many signatories are insufficient to achieve this goal, optimism prevailed in the second half of 2020. Not only did several major emitters announce net‐zero mitigation targets around mid‐century, but the new Biden Administration immediately announced the U.S.’s re‐entry into Paris and a net‐zero goal for 2050. U.S. federal re‐engagement in climate action could have a considerable impact on its national greenhouse gas emissions pathway, by significantly augmenting existing state‐level actions. Combined with U.S. re‐entry in the Paris Agreement, this could also serve as a stimulus to enhance ambitions in other countries. A critical question then becomes what such U.S. re‐engagement, through both national and international channels, would have on the global picture. This commentary explores precisely this question, by using an integrated assessment model to assess U.S. national emissions, global emissions, and end‐of‐century temperatures in five scenarios combining different climate ambition levels in both the U.S. and the rest of the world. Our analyses finds that ambitious climate leadership by the Biden Administration on top of enhanced climate commitments by other the major economies could potentially be the trigger for the world to fulfill the temperature goal of the Paris Agreement.

Development finance institutions (DFIs) play a key role in achieving the Paris Agreement’s goal of aligning financial flows with low-emission, climate-resilient development pathways. Many DFIs have committed to aligning their investments with the objectives of the Paris Agreement, but to date, efforts to align DFI investments have primarily focused on direct project financing. Most DFIs channel substantial portions of their finance through financial intermediaries. To be fully aligned with global climate goals, DFIs must also align these “indirect” investments. This paper proposes a robust yet practical approach for development finance institutions to follow to align their investments through financial intermediaries with the goals of the Paris Agreement.

Numerous pressures influence the ecological capacity and health of drylands globally. Shrubs are often a critical component of these systems and can function positively as foundation species through facilitation of other species. Nonetheless, limited attention has been paid to the potential negative and indirect effects of shrubs. Here, we tested the hypothesis that plant facilitation can both accelerate the invasion process and amplify the negative effects of an invader on the native community. The invasive species Bromus madritensis ssp. rubens capitalized on facilitation by resident native shrub species. This in turn further degraded California mixed grasslands by negatively impacting other annual protégé plant species in these specific microhabitats. Indirect shrub‐mediated interactions were thus a critical component of the ecological community assembly processes, and this suggests that we need to move beyond pairwise interactions to more rapidly advance grassland management and restoration theory.

ABSTRACTIdentifying high‐quality habitat (i.e., areas with resources and conditions suitable to support long‐term species persistence) is a priority for conservation, but estimating habitat quality is expensive and time consuming. Instead managers often rely on occurrence data or models of habitat suitability, but these data are only proximally related to individual and population persistence on the landscape. In most habitat suitability modeling studies, researchers treat the model as a hypothesis and the occurrence data as the truth. But occurrence does not always correlate with habitat as expected; therefore, occurrence data may be unreliable. We propose that suitability models and occurrence data be given equal weight to highlight areas of disagreement for future demographic study. To highlight this approach, we used the giant kangaroo rat (Dipodomys ingens) as a case study because their distinct burrow mounds allow for remote monitoring of short‐term presence and long‐term persistence. We conducted trapping, manned aerial surveys, and aerial imagery surveys in the San Joaquin Desert in California, USA, between 2001 and 2017 and compared the results to an existing habitat suitability model to provide estimates of long‐term persistence based on the presence of burrow mounds made by giant kangaroo rats. We treated areas of positive agreement as priorities for habitat conservation and areas of negative agreement as areas managers could ignore. Remaining areas should be prioritized for additional occupancy and demographic studies. From an initial area of 17,385 km2, we identified 668 km2of currently occupied high‐quality habitat. Of this, just 135 km2was on private land and therefore requiring protection. We classified 1,498 km2(8.6%) for additional research. Of that area, 744 km2was flagged for additional occupancy surveys. Our 3 data sets disagreed over 754 km2, suggesting a need for further demographic studies to reveal important population‐habitat relationships for the species in those areas. This approach can be useful as part of any habitat conservation exercise for prioritizing protection or targeting future demographic studies. © 2021 The Wildlife Society.

Abstract Arthropods underpin arid community dynamics and provide many key ecosystem services. In arid ecosystems, the key habitat components that influence arthropod community structure are relatively understudied. Ephedra californica is a locally abundant shrub now restricted to highly fragmented populations with established positive effects on plant and vertebrate animal communities within the drylands of Southern California. The capacity for these positive effects to further support ground arthropod communities has not been examined. We tested the hypothesis that the physical structure and cover vegetation enhance key measures of arthropod community assembly at nine Californian desert sites that comprise an extensive regional aridity gradient. We contrasted the effects of shrub canopies with ground‐covering vegetation on structuring ground‐active arthropod communities by surveying ground‐active arthropods with pitfall traps and collecting vegetation on the soil surface in the form of residual dry matter (RDM). We collected a total of 5820 individual arthropod specimens for a total of 159 morphospecies. Arthropod abundance and morphospecies richness and RDM biomass and cover were significantly greater beneath the canopy of E. californica throughout the region. Total biomass of RDM did not significantly influence arthropod communities, but cover of RDM on the soil surface negatively influenced arthropod abundance. Neither climatic aridity nor downscaled evaporative stress estimates were significant mediators of the arthropod‐vegetation association patterns. Vegetation thus likely has direct and indirect physical effects on arthropod communities. These canopy vs. soil surface vegetation differences will refine sampling of fine‐scale patterns of arthropod diversity in drylands. Regional land managers can support arthropod diversity by maintaining populations of foundation shrub species such as E. californica.

Abstract 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 and also included a population of G. sila with no access to large shrubs to facilitate comparison of the thermal ecology of G. sila populations in shrubless and shrubbed sites. 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 site had higher midday body temperatures and therefore poorer thermoregulatory accuracy than G. sila from a shrubless site, suggesting that greater surface activity may represent a thermoregulatory trade‐off 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.

Recognizing how climate change will impact populations can aid in making decisions about approaches for conservation of endangered species. The blunt-nosed leopard lizard (Gambelia sila) is a federally endangered species that, despite protection, remains in extremely arid, hot areas and may be at risk of extirpation due to climate change. We collected data on the field-active body temperatures, preferred body temperatures and upper thermal tolerance of G. sila. We then described available thermal habitat using biophysical models, which allowed us to (i) describe patterns in lizard body temperatures, microhabitat temperatures and lizard microhabitat use; (ii) quantify the lizards' thermoregulatory accuracy; (iii) calculate the number of hours they are currently thermally restricted in microhabitat use; (iv) project how the number of restricted hours will change in the future as ambient temperatures rise; and (v) assess the importance of giant kangaroo rat burrows and shade-providing shrubs in the current and projected future thermal ecology of G. sila. Lizards maintained fairly consistent daytime body temperatures over the course of the active season, and use of burrows and shrubs increased as the season progressed and ambient temperatures rose. During the hottest part of the year, lizards shuttled among kangaroo rat burrows, shrubs, and open habitat to maintain body temperatures below their upper thermal tolerance, but, occasionally, higher than their preferred body temperature range. Lizards are restricted from staying in the open habitat for 75% of daylight hours and are forced to seek refuge under shrubs or burrows to avoid surpassing their upper thermal threshold. After applying climatic projections of 1 and 2°C increases to 2018 ambient temperatures, G. sila will lose additional hours of activity time that could compound stressors faced by this population, potentially leading to extirpation.

Questions Deserts ecosystems are threatened by shifts in precipitation patterns from climate change. Positive interactions among plants could buffer desert communities from environmental extremes and resource limitations. However, to improve our ability to predict the response of plant interactions and the plant community to environmental change, we must examine the role of species identity in facilitation. Here, we asked: how do species identity, soil nutrients, and aridity drive positive interactions among plants along a regional gradient of semi-arid to hyper-arid. Location California, USA. Methods We selected seven sites located across three deserts in California that cover the geographic range of the benefactor shrubEphedra californica. In two growing seasons and within 30 pairs of shrub-open microsites at each site, we planted seeds of three annual phytometer species selected for their affinity to areas that are semi-arid, arid, or both. In each microsite, we also surveyed the composition of the annual community and measured soil nutrients. Results Shrubs facilitated the semi-arid phytometer species, reduced the hyper-arid phytometer species, and had no effect on the species found throughout the arid gradient. Shrub facilitation on community-level biomass of annual species decreased linearly with aridity to neutral interactions at the most arid sites. In the semi-arid sites, shrubs negatively affected community-level species richness and native species abundance, but increased invasive grasses. Conclusions Idiosyncratic responses of annual plant species to shrub facilitation along an aridity gradient highlight the issue in generalizing plant interactions without considering species-specific differences. Additionally, the effects of shrub facilitation appear to benefit exotic species with competitive traits which can indirectly reduce native species richness in semi-arid ecosystems. Understanding positive interactions in the context of aridity gradients can provide better insights into the expected changes in species composition that will occur as a result of climate change.