Robert Nathan Fisher

We assembled and annotated a chromosome-level genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (quality value [QV] = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This genome assembly, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

The golden eagle (Aquila chrysaetos) is an apex predator across its holarctic range. Although chromosome-level reference genome assemblies are available for two of the six golden eagle subspecies (European and Japanese), current assemblies for the North American subspecies (A. c. canadensis) were generated using short-read sequencing technology, limiting completeness, contiguity, and accuracy. Here we present a chromosome-length de novo genome assembly for a male A. c. canadensis as part of the California Conservation Genomics Project (CCGP). We used Pacific Biosciences HiFi reads and Omni-C chromatin-proximity sequencing to produce a high-quality assembly consistent with the standard CCGP reference genome protocol. Our assembly spans 1.28 Gbp and comprises 316 scaffolds with a scaffold N50 of 47.3 Mbp, a contig N50 of 30.3 Mbp, and a benchmarking universal single-copy ortholog (BUSCO) completeness score of 97.4%. This reference genome assembly offers a valuable resource for delineating genomic variation and assessing conservation needs in golden eagle populations across California and its North American range more broadly.

Predicting population abundance while accounting for uncertainty is an essential task for managers of endangered species but is often hindered by the challenge and expense of comprehensive data collection. Many traditional methods for estimating abundance of rare or elusive species are costly and logistically difficult, with occupancy‐based methods being a popular alternative. While the theoretical relationship between occupancy and abundance is well studied, there are few examples of methodological approaches for predicting abundance from occupancy. This study presents a novel approach to bridge the gap between abundance and occurrence for species with low capture probability, using the Pacific pocket mouse ( Perognathus longimembris pacificus ; PPM) in Southern California, USA, as a model system. PPM have been monitored across three subpopulations in this region using track tubes to inform occupancy over space and time and live captures to inform PPM demography and phenology. Paired capture–recapture data and presence–absence data collected between 2012 and 2022 were used to estimate density, occupancy, and detection, respectively. Density was modeled as a function of both occupancy and detection, and abundance at monthly and annual scales was predicted from estimates of density for all subpopulations. Our methodology leverages all available data in an integrated Bayesian analysis where uncertainty in site‐level abundance is naturally accounted for when scaling abundance estimates to the population level. While occupancy and detection were both predictive of and positively correlated with density, a meaningful amount of variation in density was not explained by our model, revealing avenues for future study as well as providing a realistic assessment of uncertainty in population‐level abundance predictions. In addition to advancing the current understanding of Pacific pocket mouse population dynamics, this approach is applicable to a wide array of species and ecosystems where population management is necessary, but individuals have low capture probability and available resources may preclude direct estimation of density at relevant spatial scales. From a design perspective, our results demonstrate the utility of strategically deploying density‐based monitoring methods within long‐term occupancy monitoring programs. More generally, our findings underscore the potential of this approach to inform methods to include abundance estimation in spatial occupancy monitoring programs for endangered species.

The transition from small genetic to genome-scale datasets for studying biodiversity has revealed that genetic exchange through introgressive hybridization is a widespread phenomenon in nature. Despite this, a lack of high-quality reference genomes for most non-model species limits our understanding of the impact of this process for many taxonomic groups. This restricts the range of insights that genomic tools can provide for conservation biologists, who often hope to employ genomic datasets to accurately identify historically isolated lineages to protect and to predict their evolutionary fate in the face of environmental change. Tiger whiptail lizards (Aspidoscelis tigris complex) are an abundant and important ecological component of ecosystems across the southwestern United States. In this study, we assembled and annotated a chromosome-level reference genome for A. t. stejnegeri from coastal California. We then used this reference genome to reconstruct patterns of speciation and admixture within the larger species complex, finding evidence that gene flow is widespread both geographically and across the genome.

Life history strategies vary widely among species and play a vital role in extinction risk, especially in a rapidly changing environment. For many taxa, information on life history such as longevity, lifespan, and generation time is incomplete. This is especially true for amphibians, which have experienced large‐scale declines in recent decades. The mountain yellow‐legged frog ( Rana muscosa ) is a California endemic recognized as a state and federally endangered species. We evaluated a 23‐year dataset of six wild R. muscosa populations in southern California. We calculated the average lifespan of individuals in these six populations to be approximately 9.5 years, with a mean generation time of 7.4 years. We did not detect a difference in longevity between sexes or a difference in apparent survival across various ages of adults. We also documented the longest‐lived ranid frog ever recorded from a wild population: a male R. muscosa that was at least 21 years old. Our results suggest a relatively long generation time for this species, a characteristic that may benefit them because reproduction is regularly challenged by drought, fire activity, and disease. This information is important for understanding the complex life history of this endangered ranid frog and can help guide efforts to manage and recover the species.

Two-thirds of Earth’s species have undergone population declines, leaving many vulnerable to genomic erosion and inbreeding depression. Genetic rescue can boost the fitness of small populations, but perceived risks of outbreeding depression can limit its use. We quantified these trade-offs in hundreds of endangered Pacific pocket mice ( Perognathus longimembris pacificus ) by combining whole-genome sequences with fitness data. The impacts of genomic erosion in remnant populations were reversed in an admixed breeding program, suggesting the potential benefits of genetic rescue. However, differences in chromosome numbers increase the risk of genetic incompatibilities. Fitness analyses suggested that although admixed karyotypes may have reduced fertility, non-admixed mice with low heterozygosity and high genetic load had even lower fitness, pointing to a greater risk of extinction if populations remain isolated.

Advances in genomic studies are revealing that gene flow between species is more frequent than previously understood, although the ways in which hybridization can bias gene flow across species boundaries or the extent to which introgression might be adaptive remain unexplored in most systems. We report on an annotated chromosome-level genome assembly for the Gilbert’s skink, Plestiodon gilberti, one of 18 clades of reptiles and amphibians selected for reference genome sequencing in the California Conservation Genomics Project. This assembly was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data. Although members of the Scincidae comprise nearly one-quarter of all lizard species (1785 described species), this de novo assembly represents one of only 10 skink species globally and the first North American skink with a reference genome. The assembly has a total length of ~ 1.57 Gb, a scaffold N50 length of ~ 231.32 Mb, read coverage of ~56X, and BUSCO completeness score of 97.2% based on the Tetrapoda ortholog database. Plestiodon gilberti is a member of the Plestiodon skiltonianus species complex, a group with many of the characteristics of ecological speciation but where ancient hybridization and biased introgression present challenges to retracing the initial patterns of lineage divergence. Combined with dense sampling of resequenced genomes in the California Conservation Genomics Project, including other members of the P. skiltonianus complex, this reference genome will enable future analyses of the links between divergent selection and the genes underlying speciation, as well as the potential for introgression to enable adaptation to new or changing environments.

Climate change significantly affects precipitation patterns at multiple scales, which influences river and other hydrologic flow regimes. However, the impacts of climate‐driven changes to hydrologic regimes on the vulnerability of species associated with riparian areas remain largely unexplored. Not considering the effect of flow alteration compromises the ability to identify and protect critical habitat areas. We developed a species distribution model to predict the distribution of an endangered amphibian (arroyo toad, Anaxyrus californicus ) under current and future climate‐impacted flow scenarios to better understand its vulnerability to altered conditions. The current modeled distribution of the arroyo toad was compared to models that estimated flows altered through stochastic changes in air temperature and precipitation associated with climate change. To analyze vulnerability, we investigated disparities in elevation, range size, range overlap, protected range, and predicted probability of occurrence. The study identified key flow metrics associated with toad habitats, emphasizing a negative relationship with most, aligning with arroyo toad breeding requirements. Vulnerability assessments demonstrated a potential reduction in toad range and shifts in elevational range potentially due to climate‐induced flow alterations. Our study underscores the importance of managing altered flow to support freshwater ecosystems, allowing managers to prioritize conservation efforts, protect vulnerable streams, and address problematic areas. However, additional factors like geomorphology and human activities also play significant roles, suggesting the need for diverse management strategies.

Disease, alone or combined with other stressors such as habitat loss and contaminants, affects wildlife populations worldwide. However, interactions among stressors and how they affect demography and populations remain poorly understood. The amphibian chytrid fungus (Batrachochytrium dendrobatidis; Bd) is a sometimes-lethal pathogen linked with population declines and extirpations of amphibians globally. Laboratory evidence shows ubiquitous contaminants like methylmercury (MeHg) can reduce vigor and survival of amphibians, but population-level effects remain unclear. We used non-lethal sampling to assess how Bd and MeHg affected survival of juvenile and adult amphibians in 20 populations across the USA. Survival of several species declined with increasing Bd loads, including some species previously considered resistant to Bd (e.g., eastern newt [Notophthalmus viridescens]). Although our sampling for MeHg was less intensive than for Bd, we found MeHg can both directly reduce survival and synergistically magnify the effects of Bd infection. For a population of foothill yellow-legged frogs (Rana boylii), the estimated reduction in survival from MeHg exceeded that from Bd. Although effects varied widely among populations and species, our results help clarify the potential for synergistic effects of disease and contaminants and emphasize the complexity of identifying and quantifying the population-level effects of interactions among stressors.