Muskox (Ovibos moschatus, Zimmermann 1780), or Umingmak (in Inuktitut), is a critical component of the terrestrial Arctic ecosystem. In many regions, muskoxen are key to Inuit food security and important to cultural identity, while also providing economic opportunity. Although muskox populations in Greenland and part of Canada appear to be thriving, others are experiencing an uncertain future. A comprehensive understanding of factors driving demographic change, including Indigenous and western science-based knowledge of muskox biology and the Arctic ecosystem in which it lives, is necessary to safeguard populations in the crosshairs of climate change. The inclusion of genomic (or DNA-based) tools into management is predicated on Inuit needs and the amenability of such tools for co-development with Indigenous and scientific partners. The Muskox and Genomics in the Community (MAGIC) workshop was held in Cambridge Bay, Nunavut in January 2024, providing a cross-cultural grounding for discussion on the co-development of genomic tools for muskox conservation and management. Outcomes included forging opportunities for co-learning and knowledge exchange around genomics science and Inuit traditional ecological knowledge, identification of relevant species for whole genome sequencing, documentation of knowledge gaps in muskox biology, and laying conceptual foundations for the co-development of genomics tools based on Inuit Qaujimajatuqangit.

Global spread of animal pathogens has contributed to species declines and extinctions. In regions where a particular disease is enzootic, pathogen inhibition may arise through protection provided by host-associated microbiomes. Amphibians skin microbiomes can inhibit growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd), preventing emergence of disease through a range of microbe-mediated antifungal mechanisms, allowing hosts to resist Bd infection. However, it remains unclear how skin microbiomes may shift in community composition or structure following infection by different Bd strain types. We assessed infection dynamics of Bd-resistant amphibians (Ambystoma maculatum) following experimental exposure to enzootic and epizootic strains of Bd-GPL and tracking pathogen load and bacterial skin microbiome community responses from exposure through to recovery, using 16S rRNA metabarcoding. We found that microbiome communities shifted post-exposure, with increasing diversity, dominance, abundance and total proportion of known Bd-inhibitory microbes, indicating microbial rescue effects during infection. We also observed lower intra-host variation in diversity during recovery, indicating a shared functional response across the host population and broadly indicative of microbial community resilience. Salamanders exposed to enzootic Bd had greater pathogen loads over time and demonstrated more prolonged community changes and more putatively protective microbiomes, whereas epizootic Bd infection was more rapidly cleared following temporary increase in inhibitory microbes. Collectively, these results indicate that skin microbiomes may offer a crucial barrier to fungal disease in Bd-resistant amphibians, with exposure to pathogens inducing changes in microbial community structure that benefit hosts, possibly driven by localized coevolutionary changes in infection dynamics. Our work illustrates how complex host-pathogen interactions are mediated by skin microbiomes through changes in microbial community dynamics that favour pathogen resistant microbes.

Respiratory disease outbreaks with overlapping symptomology in long-term care and congregate living facilities can have disproportionately negative impacts on the health and well-being of residents. Wastewater surveillance of SARS-CoV-2 demonstrated efficacy as an early outbreak warning for congregate facilities allowing for the implementation of effective non-pharmaceutical interventions. Assays that concomitantly target multiple respiratory pathogens exist for clinical diagnosis; however, challenges remain in the implementation of similar multi-pathogen surveillance from wastewater in terms of specificity, sensitivity and connections to clinical data. Herein, RT-qPCR multiplex assays were developed, combining detection of SARS-CoV-2, influenza and respiratory syncytial virus (RSV) into a single assay, reducing time and cost per sample. Data were analyzed in context of single pathogen detection sensitivity and known outbreaks at 1 long-term care facility, 4 retirement homes and 1 community site in Peterborough, ON, Canada. Analyses focused on 8 outbreak periods (SARS-CoV-2 (6); influenza (1); RSV (1)), 2 suspected influenza outbreaks, and parallel respiratory outbreaks. Wastewater signals for pathogens correlated with reported outbreak periods at facilities, while relative sensitivity was reduced, multiplex assay results had comparable signal trends to that of single pathogen assays. Among SARS-CoV-2 outbreaks, wastewater signals were detected ∼ 3-4 days prior to outbreaks. For influenza and RSV outbreaks, consistent wastewater signals were detected 3 and 12 days prior, respectively. A multiplexed assay approach allowed for identification of parallel respiratory pathogen outbreaks with overlapping symptomology. These findings support wastewater surveillance and efficiencies of multiplexing respiratory virus detection without losing signal detection for ongoing reduced-cost monitoring programs.

Gut microbiomes play critical roles in host-environment interactions, reflecting habitat and foraging niches. North American bison (Bison bison) subspecies—plains bison (B. bison bison) and wood bison (B. bison athabascae)—exhibit limited genetic variation from historic population bottleneck events, potentially undermining their evolutionary potential. Understanding variation in gut microbiota composition between subspecies may shed light on genetic, phenotypic, and ecological divergence relevant to their adaptive capacities. Using 16S rRNA metabarcoding of fecal samples, we characterized the gut microbiota of both subspecies in the sympatric environment of Elk Island National Park, providing insight into potential phylogenetic gut microbiome divergence. Like other ruminants, the gut microbial community of both subspecies consists primarily of the bacterial phyla Firmicutes and Bacteroidetes. Subspecific classification explained no significant differences in alpha diversity (p > 0.05) in the overall dataset, but has a potentially significant effect on beta diversity (p < 0.05, R2 = 0.04). Gut microbiota divergence between subspecies may be driven by differential abundance of specific taxa and associated functional pathways, likely influenced by dietary preferences, ancestral phenotypes, and historical ranges. Our findings support further investigation into diet-microbiome relationships between subspecies in sympatric environments and metagenomic approaches to explore functional differences in the gut microbiome.

Reliable and comparable data from multiple laboratories are essential for networks relying on reverse transcription quantitative polymerase chain reaction (RT-qPCR)-based surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic material in wastewater. Large-scale networks, such as those spanning Canada and the United States, depend on multiple laboratories deploying varied methods. However, the comparability of these methods and implications for data interoperability have not been rigorously examined. Split-sample results from an inter-laboratory study conducted across 15 laboratory methods over 15 rounds in Canada were analyzed. This study focused on assessing the consistency of SARS-CoV-2 signal levels, as well as an indicator of fecal content, Pepper Mild Mottle Virus (PMMoV). Linear mixed models and associated intraclass correlation coefficients (ICC) were applied to gain insights to inter and intra-laboratory method variability. Wastewater SARS-CoV-2 signal levels were moderately concordant across laboratories, even without a single standardized protocol (ICC ≈ 0.70, p < 0.01). Laboratories generally distinguished and aligned on different levels of SARS-CoV-2 present in wastewater samples. However, assays targeting PMMoV displayed significant method-specific variability (ICC = 0.22, p < 0.01). This variability may be attributable to differences in standard quantification materials and different partitioning behaviour of PMMoV relative to SARS-CoV-2 within wastewater matrices. These results highlight the robustness of SARS-CoV-2 surveillance methods across laboratories, demonstrating reliable data comparability despite methodological differences. In contrast, PMMoV assays exhibited greater methodological variability, thereby inflating inter-lab PMMoV-normalized SARS-CoV-2 variability. This suggests the need for careful evaluation of the purpose of-and scale at-which PMMoV normalization is applied. Insights into the impacts of SARS-CoV-2 mutations on assay performance highlight the necessity of routine evaluation to ensure methods remain reliable and fit-for-purpose.

During the COVID-19 pandemic, the Province of Ontario, Canada, launched a wastewater surveillance program to monitor SARS-CoV-2, inspired by the early work and successful forecasts of COVID-19 waves in the city of Ottawa, Ontario. This manuscript presents a dataset from January 1, 2021, to March 31, 2023, with RT-qPCR results for SARS-CoV-2 genes and PMMoV from 107 sites across all 34 public health units in Ontario, covering 72% of the province's and 26.2% of Canada's population. Sampling occurred 2-7 times weekly, including geographical coordinates, serviced populations, physico-chemical water characteristics, and flowrates. In doing so, this manuscript ensures data availability and metadata preservation to support future research and epidemic preparedness through detailed analyses and modeling. The dataset has been crucial for public health in tracking disease locally, especially with the rise of the Omicron variant and the decline in clinical testing, highlighting wastewater-based surveillance's role in estimating disease incidence in Ontario.

One method of estimating the post mortem interval (PMI) is to use the oldest stage of immature blow flies on or surrounding a corpse to determine the minimum PMI. When finished feeding, larvae leave a carcass to pupate in the surrounding soil, and can be difficult to find. We investigated if flat and undulating terrain affect how far Lucilia illustris larvae disperse after feeding. We hypothesized that post-feeding larvae disperse over undulating and flat terrain about the same travel distance. However, because larvae must crawl up and downhill in undulating terrain they end up pupating in soil closer to the originating carcass than larvae that crawled over flat terrain. We tested this in a field study using pig half-heads placed on sand which had two surface treatments, flat sand and sand with 2.5 cm undulations. We allowed blow flies to lay eggs on the half-heads, took soil core samples at various distances, then allowed adults to emerge in the lab. In undulating terrain, while more adults emerged from soil cores closer to carcasses than from soil core from flat terrain. However, net travel path lengths were similar for both treatments.

We present a genome assembly of Caretta caretta (the Loggerhead sea turtle; Chordata, Testudines, Cheloniidae), generated from genomic data from two unrelated females. The genome sequence is 2.13 gigabases in size. The assembly has a busco completion score of 96.1% and N50 of 130.95 Mb. The majority of the assembly is scaffolded into 28 chromosomal representations with a remaining 2% of the assembly being excluded from these.

Demand for bear bile, a prized component of traditional Asian medicines, threaten Asiatic and sun bear population sustainability. While laws exist to prevent poaching and trafficking of bear parts and derivatives, smuggling persists with demand extending to surrogate species, including American black bears (Ursus americanus). Mitochondrial DNA (mtDNA) sequencing can identify products putatively containing biological bear material but can be undermined by PCR inhibitors in bile and a lack of sensitivity at trace levels. Quantitative PCR (qPCR) assays can be used to distinguish between closely related target species, while concomitantly evaluating inhibition and false negative results in low quality/quantity DNA applications. Herein, we develop a multiplexed qPCR assay to detect and differentiate among bear species, including highly diluted bile samples mixed within liquors as common dilutants. The assay detects as little as 10 locus copies/reaction of bear DNA with 95% confidence, distinguishing among sun, Asiatic and American black bears. Demonstrating the sensitivity and applicability of this assay in context of current bile mixture recipes, dilutions of 1:5,000 bile with ethanol, red wine, and spirits, all yielded clear quantifiable detections, where our data suggests as little as 1 drop of bile per 750 mL bottle of alcohol would still exceed the limits of detection (e.g., 1:15000 dilution or <0.05 mL bile per 750 mL bottle). Overall, this study provides a rapid, sensitive, and specific test to identify and distinguish among bear species commonly used for bile production to aid wildlife enforcement applications.

Documenting biodiversity, species occurrence, and species status require reliable monitoring techniques, but the complex life history and cryptic behavior of many anurans create challenges for conventional monitoring approaches. Environmental DNA (eDNA) surveys are a promising alternative (or complement) to conventional anuran monitoring, but their relative success has not been fully tested. We assessed the comparative efficacy of targeted eDNA detection via quantitative PCR (qPCR) and three conventional amphibian survey methods (visual encounter, breeding call, and larval dipnet surveys) for detecting nine anuran species in natural wetlands in southern Ontario, Canada. Our analyses revealed that all assessment methods yielded imperfect detection, with visual encounter and eDNA surveys detecting the greatest species richness and eDNA surveys requiring the fewest sampling events. Amphibian community composition results differed among survey methods and sampling events, and detection efficacy was markedly variable, with some species requiring two to three methods to maximize detection success. Notably, two relatively terrestrial species (Anaxyrus americanus and Hyla versicolor) had relatively low and seasonally variable eDNA detection rates, suggesting that species-specific ecology likely affects eDNA presence or detection. These findings suggest that optimized monitoring for complex anuran communities may require application of multiple monitoring methods, which may need to be tailored to individual target species or communities.

We present a genome assembly of Caretta caretta (the Loggerhead sea turtle; Chordata, Testudines, Cheloniidae), generated from genomic data from two unrelated females. The genome sequence is 2.13 gigabases in size. The assembly has a busco completion score of 96.1% and N50 of 130.95 Mb. The majority of the assembly is scaffolded into 28 chromosomal representations with a remaining 2% of the assembly being excluded from these.

Southeastern Canada is inhabited by an amalgam of hybridizing wolf-like canids, raising fundamental questions regarding their taxonomy, origins, and timing of hybridization events. Eastern wolves (Canis lycaon), specifically, have been the subject of significant controversy, being viewed as either a distinct taxonomic entity of conservation concern or a recent hybrid of coyotes (C. latrans) and grey wolves (C. lupus). Mitochondrial DNA analyses show some evidence of eastern wolves being North American evolved canids. In contrast, nuclear genome studies indicate eastern wolves are best described as a hybrid entity, but with unclear timing of hybridization events. To test hypotheses related to these competing findings we sequenced whole genomes of 25 individuals, representative of extant Canadian wolf-like canid types of known origin and levels of contemporary hybridization. Here we present data describing eastern wolves as a distinct taxonomic entity that evolved separately from grey wolves for the past ∼67,000 years with an admixture event with coyotes ∼37,000 years ago. We show that Great Lakes wolves originated as a product of admixture between grey wolves and eastern wolves after the last glaciation (∼8,000 years ago) while eastern coyotes originated as a product of admixture between "western" coyotes and eastern wolves during the last century. Eastern wolf nuclear genomes appear shaped by historical and contemporary gene flow with grey wolves and coyotes, yet evolutionary uniqueness remains among eastern wolves currently inhabiting a restricted range in southeastern Canada.

Diseases vary among and within species but the causes of this variation can be unclear. Immune responses are an important driver of disease variation, but mechanisms on how the body resists pathogen establishment before activation of immune responses are understudied. Skin surfaces of mammals are the first line of defense against abiotic stressors and pathogens, and skin attributes such as pH, microbiomes, and lipids influence disease outcomes. Sebaceous glands produce sebum composed of multiple types of lipids with species-specific compositions. Sebum affects skin barrier function by contributing to minimizing water loss, supporting thermoregulation, protecting against pathogens, and preventing UV-induced damage. Sebum also affects skin microbiome composition both via its antimicrobial properties, and by providing potential nutrient sources. Intra- and interspecific variation in sebum composition influences skin disease outcomes in humans and domestic mammal species but is not well-characterized in wildlife. We synthesized knowledge on sebum function in mammals in relation to skin diseases and the skin microbiome. We found that sebum composition was described for only 29 live, wild mammalian species. Sebum is important in dermatophilosis, various forms of dermatitis, demodicosis, and potentially white-nose syndrome. Sebum composition likely affects disease susceptibility, as lipid components can have antimicrobial functions against specific pathogens. It is unclear why sebum composition is species-specific, but both phylogeny and environmental effects may drive differences. Our review illustrates the role of mammal sebum function and influence on skin microbes in the context of skin diseases, providing a baseline for future studies to elucidate mechanisms of disease resistance beyond immune responses.

Microbiome diversity and diet composition concomitantly influence species health, fitness, immunity, and digestion. In environments where diet varies spatially and temporally, microbiome plasticity may promote rapid host adaptation to available resources. For northern ungulates in particular, metabarcoding of noninvasively collected fecal pellets presents unprecedented insights into their diverse ecological requirements and niches by clarifying the interrelationships of microbiomes, key to deriving nutrients, in context of altered forage availability in changing climates. Muskoxen (Ovibos moschatus) are Arctic-adapted species that experience fluctuating qualities and quantities of vegetation. Geography and seasonality have been noted to influence microbiome composition and diversity in muskoxen, yet it is unclear how their microbiomes intersect with diet. Following observations from other species, we hypothesized increasing diet diversity would result in higher microbiome diversity in muskoxen. We assessed diet composition in muskoxen using three common plant metabarcoding markers and explored correlations with microbiome data. Patterns of dietary diversity and composition were not fully concordant among the markers used, yet all reflected the primary consumption of willows and sedges. Individuals with similar diets had more similar microbiomes, yet in contrast to most literature, yielded negative relationships between microbiome and diet alpha diversity. This negative correlation may reflect the unique capacities of muskoxen to survive solely on high-fiber Arctic forage and provide insight into their resiliency to exploit changing dietary resources in a rapidly warming Arctic altering vegetation diversity.

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The coronavirus disease 2019 (COVID-19) pandemic has disproportionately affected seniors living in congregate living settings. The evolving surveillance context has led to novel use of wastewater surveillance to monitor levels of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in these settings. This study presents a pilot of upstream congregate living wastewater surveillance of SARS-CoV-2 for the detection of COVID-19 outbreaks and the effects of early public health interventions. We monitored localized wastewater SARS-CoV-2 levels from four congregate living settings March 15, 2021 to October 1, 2022 and correlated these levels with suspected and confirmed COVID-19 outbreaks determined by other methods. We identified five wastewater signals that correlated with confirmed outbreaks and three wastewater signals that did not correlate with subsequent outbreaks. In the five confirmed outbreaks, the wastewater signal was detected 2-10 days (median, five days) prior to confirmation of the outbreak by case testing. This pilot demonstrates upstream sampling for SARS-CoV-2 in wastewater may effectively detect outbreaks prior to their detection through symptomatic case testing and could support a balanced approach to outbreak response in congregate living settings, leading to increased wellbeing of these residents.

Characterizing patterns and drivers of dispersal is fundamental to our understanding of animal ecology and ultimately informing species conservation and management strategies. In this study, we used microsatellite data from 3941 individual black bears Ursus americanus occupying 73 spatially distinct sampling areas across a large heterogeneous landscape to characterize dispersal via gene flow directionality. We fit spatial models to quantified gene flow to test hypotheses regarding drivers of putative dispersal patterns. Specifically, we tested the relative influence of food productivity gradients, bear density, and bear harvest on dispersal. We also evaluated differences in gene flow patterns within and between sexes to assess sex‐biased dispersal. We found evidence suggestive of positive density‐dependent, male‐biased dispersal. Our data show evidence of a relationship between dispersal and broad food productivity gradients. Specifically, male bears displayed preferential dispersal towards mixed deciduous forests with higher food productivity relative to less productive boreal forests. Given the dense sampling scheme across a continuous population, occupying a large heterogeneous landscape, these results provide key insight as to the likely drivers of dispersal patterns in a wide‐ranging mammal.

Abstract Wastewater-based surveillance of SARS-CoV-2 RNA has been implemented at building, neighbourhood, and city levels throughout the world. Implementation strategies and analysis methods differ, but they all aim to provide rapid and reliable information about community COVID-19 health states. A viable and sustainable SARS-CoV-2 surveillance network must not only provide reliable and timely information about COVID-19 trends, but also provide for scalability as well as accurate detection of known or unknown emerging variants. Emergence of the SARS-CoV-2 variant of concern Omicron in late Fall 2021 presented an excellent opportunity to benchmark individual and aggregated data outputs of the Ontario Wastewater Surveillance Initiative in Canada; this public health-integrated surveillance network monitors wastewaters from over 10 million people across major population centres of the province. We demonstrate that this coordinated approach provides excellent situational awareness, comparing favourably with traditional clinical surveillance measures. Thus, aggregated datasets compiled from multiple wastewater-based surveillance nodes can provide sufficient sensitivity (i.e., early indication of increasing and decreasing incidence of SARS-CoV-2) and specificity (i.e., allele frequency estimation of emerging variants) with which to make informed public health decisions at regional- and state-levels.

Abstract Environmental DNA (eDNA) monitoring is rapidly becoming an established approach for detecting the presence of aquatic organisms and may also be useful for indexing or estimating species abundance. However, the link between eDNA concentration and abundance of individuals (i.e., density or biomass) remains tenuous and may vary widely across species and environmental conditions. We investigated the relationship between eDNA concentration and abundance in two common and closely related amphibians in eastern North America, the wood frog (Rana sylvatica), and northern leopard frog (R. pipiens). We manipulated tadpole density in 80‐L mesocosms and documented the relationship between tadpole density and biomass and eDNA concentration through time. The two species differed in the amount of detectible genetic material produced, despite having comparable biomass. Concentration of eDNA increased with tadpole numbers and was primarily correlated with tadpole density in wood frogs and biomass in leopard frogs. eDNA degradation rates were rapid and comparable between species, with tadpoles becoming indetectable within 5 days post‐removal from the mesocosm, irrespective of tadpole density. Overall, our findings support that eDNA concentration has potential for tracking amphibian abundance in wetlands, but that indices of abundance are likely to be coarse and species‐specific calibration will be required. Future research should address how biotic and abiotic factors influence eDNA production, degradation, and recovery across species and through time before relying on eDNA for monitoring amphibian abundance in nature.