Devaughn Fraser

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.

The guano of insectivorous bats holds ecological information that can be assessed non-invasively to characterize the gut microbiome and diet, alongside environmental microbes and pathogens of conservation concern. Despite this potential, how guano communities change during decomposition remains understudied, particularly inside anthropic roosts rather than caves. In this study, guano from little brown bat (Myotis lucifugus) colonies was sampled monthly across the summer maternity season from three sites across two locations in Connecticut, USA, at fresh deposition and at 4, 8, and 12 weeks following deposition. Resolving these cross-kingdom signals required five workflows: short-read 16S and ITS2 amplicon sequencing (Illumina) for bacterial and fungal profiling, long-read CO1 metabarcoding (Oxford Nanopore) for arthropod diet in fresh samples, long-read shotgun metagenomics for viral identification in aged samples, and targeted qPCR for organisms of bat, human, and forest-health concern. Fresh guano generated a consistent bacterial signal across sites, whereas fresh fungal communities differed by site. Responses to decomposition depended on roost setting: exterior sites lost fungal diversity and shifted toward environmental aerobes over time, while the interior roost retained the fresh sample profile. Dietary composition varied temporally, was dominated by Diptera, and included the invasive emerald ash borer (Agrilus planipennis). Pseudogymnoascus destructans, the causal agent of white-nose syndrome, occurred in fresh and aged samples at all three sites but persisted for 12 weeks only at the interior roost, where antifungal bacterial taxa were depleted. Long-read shotgun metagenomics of aged guano recovered roughly 100 viral species, predominantly bacteriophages, alongside non-bacteriophage mastadenoviruses associated with humans, bats, and other mammals. These results show that anthropic structures influence the trajectory of guano microbiome succession, and that maternity colony guano enables non-invasive assessment of environmental pathogens, bat diet, and bacterial and fungal communities.

Townsend’s big-eared bat, Corynorhinus townsendii, is a cave- and mine-roosting species found largely in western North America. Considered a species of conservation concern throughout much of its range, protection efforts would greatly benefit from understanding patterns of population structure, genetic diversity, and local adaptation. To facilitate such research, we present the first de novo genome assembly of C. townsendii as part of the California Conservation Genomics Project (CCGP). Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technologies were used to produce a de novo genome assembly, consistent with the standard CCGP reference genome protocol. This assembly comprises 391 scaffolds spanning 2.1 Gb, represented by a scaffold N50 of 174.6 Mb, a contig N50 of 23.4 Mb, and a benchmarking universal single-copy ortholog (BUSCO) completeness score of 96.6%. This high-quality genome will be a key tool for informed conservation and management of this vulnerable species in California and across its range.

The Yuma myotis bat (Myotis yumanensis) is a small vespertilionid bat and one of 52 species of new world Myotis bats in the subgenus Pizonyx. While M. yumanensis populations currently appear relatively stable, it is one of twelve bat species known or suspected to be susceptible to white-nose syndrome, the fungal disease causing declines in bat populations across North America. Only two of these twelve species have genome resources available, which limits the ability of resource managers to use genomic techniques to track the responses of bat populations to white-nose syndrome generally. Here we present the first de novo genome assembly for Yuma myotis, generated as a part of the California Conservation Genomics Project (CCGP). The M. yumanensis genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. This high-quality genome is one of the most complete bat assemblies available, with a contig N50 of 28.03 Mb, scaffold N50 of 99.14 Mb and BUSCO completeness score of 93.7%. The Yuma myotis genome provides a high quality resource that will aid in comparative genomic and evolutionary studies, as well as inform conservation management related to white-nose syndrome.

Emerging infectious diseases are significant threats to wildlife conservation, yet the impacts of pathogen exposure and infection can vary widely among host species. As such, conservation biologists and disease ecologists have increasingly aimed to understand species‐specific host susceptibility using molecular methods. In particular, comparative gene expression assays have been used to contrast the transcriptomic responses of disease‐resistant and disease‐susceptible hosts to pathogen exposure. This work usually assumes that the gene expression responses of disease‐resistant species will reveal the activation of molecular pathways contributing to host defence. However, results often show that disease‐resistant hosts undergo little gene expression change following pathogen challenge. Here, we discuss the mechanistic implications of these “null” findings and offer methodological suggestions for future molecular studies of wildlife disease. First, we highlight that muted transcriptomic responses with minimal immune system recruitment may indeed be protective for nonsusceptible hosts if they limit immunopathology and promote pathogen tolerance in systems where susceptible hosts suffer from genetic dysregulation. Second, we argue that overly narrow investigation of responses to pathogen exposure may overlook important, constitutively active molecular pathways that underlie species‐specific defences. Finally, we outline alternative study designs and approaches that complement interspecific transcriptomic comparisons, including intraspecific gene expression studies and genomic methods to detect signatures of selection. Collectively, these insights will help ecologists extract maximal information from conservation‐relevant transcriptomic data sets, leading to a deeper understanding of host defences and, ultimately, the implementation of successful conservation interventions.

Anticoagulant rodenticides (ARs) are indiscriminate toxicants that threaten nontarget predatory and scavenger species through secondary poisoning. Accumulating evidence suggests that AR exposure may have disruptive sublethal consequences on individuals that can affect fitness. We evaluated AR‐related effects on genome‐wide expression patterns in a population of bobcats in southern California. We identify differential expression of genes involved in xenobiotic metabolism, endoplasmic reticulum stress response, epithelial integrity and both adaptive and innate immune function. Further, we find that differential expression of immune‐related genes may be attributable to AR‐related effects on leucocyte differentiation. Collectively, our results provide an unprecedented understanding of the sublethal effects of AR exposure on a wild carnivore. These findings highlight potential detrimental effects of ARs on a wide variety of species worldwide that may consume poisoned rodents and indicate the need to investigate gene expression effects of other toxicants added to natural environments by humans.

Human activities threaten wildlife with a variety of novel stressors such as exposure to toxicants. Anticoagulant rodenticides (ARs) are toxicants applied worldwide and through bioaccumulation, threaten species that prey on poisoned rodents or their predators. We studied a population of urban bobcats in southern California that declined rapidly from 2002-2005 due to notoedric mange. We first assessed prevalence of AR exposure using blood and liver samples across the population and found widespread exposure (>90%). Death associated with mange was strongly correlated with cumulative first- and second-generation AR exposure. These findings suggested that exposure to both first- and second-generation ARs were an underlying cause of the disease. We next aimed to understand the sublethal immunological and physiological effects of AR exposure in this natural population. We used two approaches: 1) we used a comprehensive suite of health assays (complete blood counts, blood chemistry assessment, and immunological profiling), and 2) we quantified AR-induced differential gene expression in blood for a subset of individuals. We found that sublethal AR exposure, primarily measured as exposure to diphacinone, is associated with hallmark indicators of generalized systemic inflammation that in persistence could promote immune dysfunction. Further, differential gene expression findings supported the results of immunological profiling. Further, a decrease in the expression of genes associated with epithelial maintenance simultaneous to a decrease in gene expression linked with ectoparasitic immune response may explain the link between AR exposure and mange vulnerability. Such indirect effects of sublethal exposure exemplify the challenge of protecting wild populations from common toxicants in human-dominated environments.