Michael R. Buchalski

Novel pathogens have become a major challenge faced by wildlife in the Anthropocene. White‐nose syndrome (WNS) has decimated bat populations across North America over the last two decades. Demographic and physiological evidence of adaptation in one heavily affected species, Myotis lucifugus , has prompted multiple attempts to delineate the genomic underpinnings, but these studies show little congruence in their findings. This may be due, in part, to the limitations of the genomic resources utilized and/or analytical approaches employed. Here, we performed high‐coverage whole‐genome resequencing of M. lucifugus sampled prior to ( n = 29), and 10 years after the local arrival of WNS ( n = 30), aligned to a new reference genome to identify signatures of selection associated with adaptive responses. Using 41.9 million SNPs, we implemented a combination of hard and soft sweep detection analyses, leading to the discovery of 382 genes with robust evidence of selection. Of these, 202 (49.9%) were associated with enriched gene ontology (GO) terms, many of which were tied to neuron development, organization and function. Further, approximately half (107) of genes associated with enriched GO terms interact with genes identified by previous studies. Our findings suggest reduced susceptibility to WNS is mediated through highly complex, polygenic mechanisms. Further, we demonstrate there are far more connections among WNS selection study results than previously recognized. We believe that the methods employed by our study illustrate a need for a paradigm shift in non‐model selection studies and further highlight the value of genomics as a tool for conservation management.

Although translocations can be effective for augmenting and restoring wild populations, they can disrupt native patterns of genetic structure, diversity, and local adaptation, thereby hampering conservation efforts. Managers must weigh potential costs and benefits of choosing well‐differentiated donor individuals that could confer a boost to genetic diversity while avoiding outbreeding depression or ecological mismatch. This decision is more daunting when taxonomy is unclear or debated. For example, bighorn sheep ( Ovis canadensis ) populations in the United States that have been managed as the “California” lineage (part of the formerly recognized subspecies O. c. californiana ) originate from serial translocations sourced from populations in British Columbia, resulting in reduced genetic diversity and elevated risk of inbreeding. After research on skull shape and RFLP analysis of mtDNA failed to find support for that subspecies, some jurisdictions treated the California lineage as part of the Rocky Mountain subspecies ( O. c. canadensis ) and mixed individuals in subsequent translocations, in part to increase genetic diversity of bottlenecked populations. Yet, detailed genetic data addressing validity of those putative lineages were lacking. We reconstructed the genetic history of bighorn sheep by sampling the major putative subspecies or lineages, focusing on native (remnant) genetic variation, and generating high‐throughput DNA sequencing data (~15,000–25,000 SNPs). Complementary phylogenetic and population genetic analyses supported the distinctiveness of four bighorn lineages at levels corresponding to subspecies. Our results confirm the genetic identity of the no longer putative California bighorn lineage, answering a question that puzzled geneticists and managers for decades. Moving forward, we recommend that managers (1) maintain the natural variation held in native populations by protecting them from intentional translocations or unintentional mixing with nearby populations; (2) prioritize within‐lineage translocations for population augmentation or repatriation to previously occupied regions; and (3) cautiously consider any translocations that would lead to mixing of distinct evolutionary lineages.

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.

Nutria ( Myocastor coypus ) are semi‐aquatic rodents native to South America, introduced to the USA for fur farming during the early twentieth century. This species' herbivory can cause extensive damage to agriculture and wetland ecosystems. Though declared eradicated from California, USA, in the 1970s, nutria populations were recently discovered in the state's Central Valley and subsequently the Sacramento–San Joaquin Delta, areas of agricultural and conservation significance. We report the use of a combination of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial (mtDNA; cytochrome b locus) markers to characterize the source and demographic history of the current invasion, with the goal of informing eradication efforts. Our study is the first to develop a SNP dataset for nutria, utilizing 6809 loci to characterize genetic diversity in comparison to several potential source populations. Multivariate analysis and Bayesian clustering of the SNP dataset found the greatest similarity to invasive nutria in central Oregon, USA, with minimal genetic differentiation in the Central Valley excluding the leading edges of the invasion. Cytochrome b sequencing resulted in a single contemporary California haplotype shared with nutria in Oregon and Washington but also detected in museum samples from California fur farms predating eradication. Mantel tests found genetic differentiation among nutria in the Central Valley was best explained by ecological distance along rivers, while estimated effective migration surface ( eems ) analysis indicated gene flow was characterized by infrequent dispersal followed by rapid expansion in large, protected areas of emergent wetland habitat. These combined findings suggest contemporary California nutria represent a recent introduction that underwent rapid expansion. Our data further support treating the Central Valley as a single eradication unit while investing additional resources in targeting dispersal corridors to best achieve management goals. This study presents the first characterization of a regional nutria invasion within the larger context of global population and phylogenetics.

Mule deer (Odocoileus hemionus) is an ecologically and economically important cervid species which is widely distributed across western North America. Their broad range and use of diverse habitats, including those linked to historical glacial refugia, have made them an ideal model for studying the effects of climatic fluctuations and environmental heterogeneity on lineage diversification. The effects of this complex evolutionary history on the genome are further complicated by evidence of hybridization with other members of the genus, leading to extreme cases of mito-nuclear discordance. More recently, the influence of specific gene variants on disease dynamics, particularly the progression and morbidity of chronic wasting disease, has become an important topic of genomic research for this taxon. Here, we present and evaluate a new chromosome-level genome assembly of a representative mule deer from across the species’ diverse range as part of the California Conservation Genomics Project. We assembled a genome de novo utilizing Pacific Biosciences HiFi long-read and Omni-C chromatin-proximity sequencing data. The assembly consisted of 814 scaffolds and 901 contigs representing a contig N50 of 46.68 Mb and a scaffold N50 of 63.29 Mb. Lastly, our benchmarking universal single-copy ortholog completeness score was 96.3%. This genome represents one of the most complete Odocoileus assemblies and will further our understanding of the comparative genomic architecture of cervids.

Mountain lions, Puma concolor, are widespread and adaptable carnivores. However, due to their large home ranges and long distance dispersals, they are strongly impacted by habitat fragmentation, which results in small and isolated populations. Genomic analyses play an important role in understanding and predicting the impacts of increased isolation of populations, such as decreased genetic diversity and increased levels of inbreeding. Here we report a high-quality, chromosome-level reference genome of P. concolor that was generated as part of the California Conservation Genomics Project. The primary assembly has a total length of 2.5 Gb contained in 258 scaffolds, a contig N50 of 42.3 Mb, a scaffold N50 of 149.8 Mb, and a BUSCO completeness score of 95%. This P. concolor genome assembly will provide an important resource for genomic analyses that aid decision makers in managing the species in fragmented landscapes.

Summary Paragraph: The genus Myotis is one of the largest clades of bats, and exhibits some of the most extreme variation in lifespans among mammals alongside unique adaptations to viral tolerance and immune defense ^1–3 . To study the evolution of these phenotypes we generated cell lines and near-complete genome assemblies for eight closely related Myotis species. Using genome-wide screens of positive selection, analyses of structural variation, and functional experiments in primary cells, we identify patterns of adaptation contributing to longevity, cancer resistance, and viral interactions. We demonstrate distinct modes of adaptation to DNA and RNA viruses compared to all other mammals, with bats exhibiting genome-wide overrepresentation of positive selection for DNA virus-interacting proteins and elevated rates of copy number variation for RNA virus-interacting proteins. Characterization of Myotis- specific duplications of the key immune factor protein kinase R ( PKR ) reveals multiple ancient segregating trans-species copy number polymorphisms. We show that the recurrent evolution of longevity seen in Myotis is associated with positive selection in cancer pathways, and demonstrate a unique response to DNA damage in primary cells of the long-lived M. lucifugus . Together, our results suggest that bats’ remarkable longevity and immunity are linked through pleiotropic adaptations to viruses and aging-related disease.

A few iconic examples have proven the value of facilitated gene flow for counteracting inbreeding depression and staving off extinction, yet the practice is often not implemented for fear of causing outbreeding depression. Using genomic sequencing, climatic niche modeling, and demographic reconstruction, we sought to assess the risks and benefits of using translocations as a tool for recovery of endangered montane red fox (Vulpes vulpes) populations in the western United States. We demonstrated elevated inbreeding and homozygosity of deleterious alleles across all populations, but especially those isolated in the Cascade and Sierra Nevada ranges. Consequently, translocations would be expected to increase population growth by masking deleterious recessive alleles. Demographic reconstructions further indicated shallow divergences of less than a few thousand years among montane populations, suggesting low risk of outbreeding depression. These genomic-guided findings set the stage for future management, the documentation of which will provide a roadmap for recovery of other data-deficient taxa.

The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.