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Fountain-Jones, N. M.

Publications and source records attributed to Fountain-Jones, N. M..

11 recordsLinked to original sources

The Dominance of Geometric Graph Models in Animal Social Networks

O_LIDetecting patterns in animal social behaviour and movement is complicated by the diversity of ecological, evolutionary, environmental, and biological drivers of these behaviours such as migration, foraging, assortative mixing, socio-ecological factors, and human influence. C_LIO_LIAddressing these complexities requires a multidisciplinary approach. Recent advances in network analysis and machine learning offer powerful tools for examining and interpreting complex network structures, aiding in the identification and quantification of movement patterns and the prediction of behavioural changes. C_LIO_LIHere we use a comparative approach leveraging network analysis and machine learning techniques to assess commonalities in standard theoretical social structures governing networks across the animal kingdom. We investigate how these theoretical structures explain social organization at different scales, from entire populations to smaller groups. By leveraging interpretable machine learning techniques, we examine the predictive power of species and network construction techniques in predicting structural features of animal social networks. C_LIO_LIWe found that geometric graphs are the frequently predicted network model across the animal kingdom. These graphs represent both spatial and social processes and are formed by positioning individuals uniformly on a 2D plane, with links established based on proximity within a specified distance. In particular, geometric graphs demonstrate structural similarities with interaction types and data collection methods. For example, we found that this graph model had strong structural similarities with networks derived from physical contact and spatial proximity data. Networks with small-world properties, in contrast, were rare across all interaction types and collection methods. Additionally, the occurrence of these networks is influenced by the identity of species and sampling duration. Although incorporating species identity into the classification model did not improve the accuracy of the prediction, it enabled us to account for the varying dependencies of biological characteristics on specific behaviours. C_LIO_LIThis study highlights the value of predictive modelling for uncovering ecological drivers of animal network structures. By focusing on standard theoretical models that are well established in network science, we connect animal social networks to broader theoretical findings, while recognizing that more tailored models combining multiple generative models or network properties may offer deeper insights into network structures. We also emphasize the importance of considering how the specific methods used to build networks for each taxon could influence the biological inferences that can be drawn from those networks. C_LI

ecology↗

Positive associations matter: microbial relationships drive tick microbiome composition

Untangling how factors such as environment, host, associations between species and dispersal predict microbial dynamics is a fundamental challenge. In this study, we use a robust sampling design coupled with complementary machine-learning approaches to quantify the relative role of these factors in shaping microbiome variation of the blacklegged tick Ixodes scapularis. I. scapularis is the most important vector for Borrelia burgdorferi. (the causative agent for Lyme disease) in the U.S as well as a range of other important zoonotic pathogens. Yet the relative role of the interactions between pathogens and symbionts compared to other ecological forces is unknown. We found that positive associations between microbes where the occurrence of one microbe increases the probability of observing another, including between both pathogens and symbionts, was by far the most important factor shaping the tick microbiome. Microclimate and host factors played an important role for a subset of the tick microbiome including Borrelia (Borreliella) and Ralstonia, but for the majority of microbes, environmental and host variables were poor predictors at a regional scale. This study provides new hypotheses on how pathogens and symbionts might interact within tick species, as well as valuable predictions for how some taxa may respond to changing climate.

microbiology↗

Automated analysis of PD1 and PDL1 in lymph nodes and the microenvironment of transmissible tumors in Tasmanian devils

The wild Tasmanian devil (Sarchophilus harrisii) population has suffered a devastating decline due to two clonal transmissible cancers. Devil facial tumor 1 (DFT1) was first observed in 1996, followed by a second genetically distinct transmissible tumor, devil facial tumor 2 (DFT2), in 2014. DFT1/2 frequently metastasize, with lymph nodes being common metastatic sites. Downregulation of MHC-I by DFT1 cells is a primary means of evading allograft immunity aimed at polymorphic MHC-I proteins. DFT2 cells constitutively express MHC-I, and MHC-I is upregulated on DFT1/2 cells by interferon gamma, suggesting other immune evasion mechanisms may contribute to overcoming allograft and anti-tumor immunity. Human clinical trials have demonstrated PD1/PDL1 blockade effectively treats patients showing increased expression of PD1 in tumor draining lymph nodes, and PDL1 on peritumoral immune cells and tumor cells. The effects of DFT1/2 on systemic immunity remain largely uncharacterized. This study applied the open-access software QuPath to develop a semiautomated pipeline for whole slide analysis of stained tissue sections to quantify PD1/PDL1 expression in devil lymph nodes. The QuPath protocol provided strong correlations to manual counting. PD-1 expression was approximately 10-fold higher than PD-L1 expression in lymph nodes and was primarily expressed in germinal centers, whereas PD-L1 expression was more widely distributed throughout the lymph nodes. The density of PD1 positive cells was increased in lymph nodes containing DFT2 metastases, compared to DFT1. This suggests PD1/PDL1 exploitation may contribute to the poorly immunogenic nature of transmissible tumors in some devils and could be targeted in therapeutic or prophylactic treatments.

immunology↗

The spectral underpinnings of pathogen spread on animal networks

Predicting what factors promote or protect populations from infectious disease is a fundamental epidemiological challenge. Social networks, where nodes represent hosts and edges represent direct or indirect contacts between them, are important in quantifying these aspects of infectious disease dynamics. However, how network structure and epidemic parameters interact in empirical networks to promote or protect animal populations from infectious disease remains a challenge. Here we draw on advances in spectral graph theory and machine learning to build predictive models of pathogen spread on a large collection of empirical networks from across the animal kingdom. We show that the spectral features of an animal network are powerful predictors of pathogen spread for a variety of hosts and pathogens and can be a valuable proxy for the vulnerability of animal networks to pathogen spread. We validate our findings using interpretable machine learning techniques and provide a flexible web application for animal health practitioners to assess the vulnerability of a particular network to pathogen spread.

ecology↗

Evaluation of oral baits and distribution methods for Tasmanian devils (Sarcophilus harrisii)

ContextDiseases are increasingly contributing to wildlife population declines. Tasmanian devil (Sarcophilus harrisii) populations have locally declined by 82% largely due to the morbidity and mortality associated with two independent transmissible devil facial tumours (DFT1 and DFT2). Toxic baits are often used as a management tool for controlling vertebrate pest populations in Australia, but in other areas of the world oral baits are also used to deliver vaccines or pharmaceuticals to wildlife. Oral vaccine bait products have been distributed for more than 50 years at a landscape scale to protect wildlife from rabies virus and contributed to the elimination of fox rabies from more than ten European nations. An oral bait vaccine to protect against devil facial tumours has been proposed as a management tool to improve the population health, resiliency and fitness of wild Tasmanian devils. AimOur goal was to evaluate the potential use of edible baits as vehicles for vaccine delivery to Tasmanian devils. MethodWe tested placebo versions of baits that are already used in Australia. Key resultsCaptive devils consumed all types of placebo baits but exhibited a preference for ruminant- and fish-based baits. Captive devils also consumed inert capsules inserted into placebo baits. Bait fate trials in the field revealed that baits were generally removed within 24 hours. Tasmanian pademelons (Thylogale billardierii), brushtail possums (Trichosurus vulpecula), and Eastern quolls (Dasyurus viverrinus) were the most common nontarget bait competitors at six private properties in southern Tasmania; wild devils removed approximately 5% of ground baits at these sites. We also evaluated an automated bait dispenser, which reduced nontarget uptake and resulted in over 50% of the baits being removed by devils. ConclusionsThis study demonstrates that captive and wild devils will accept and consume placebo versions of commercial baits. Bait dispensers or modified baits or baiting strategies are needed to increase bait uptake by devils. ImplicationsBait dispensers can be used at a regional scale to deliver baits to Tasmanian devils. These could act as vehicles for preventive or therapeutic vaccines to mitigate the impacts of disease on devil populations. Short summaryThis study aimed to test oral baits as potential vaccine delivery vehicles for Tasmanian devils. Captive and wild devils consumed placebo versions of commercial baits used on mainland Australia. Abundant non-target species, such as brushtail possums, Tasmanian pademelons, and eastern quolls consumed most baits in the wild. Implementation of automated bait dispensers increased bait uptake by devils to over 50% at the same regional field sites.

zoology↗

Strong trait correlation and phylogenetic signal in North American ground beetle (Carabidae) morphology

Functional traits mediate species responses to and roles within their environment, and are constrained by evolutionary history. While we have a strong understanding of trait evolution for macro-taxa such as birds and mammals, our understanding of invertebrates is comparatively limited. Here we address this gap in North American beetles with a sample of ground beetles (Carabidae), leveraging a large-scale collection and digitization effort by the National Ecological Observatory Network (NEON). For 154 ground beetle species, we measured seven morphological traits, which we placed into a recently-developed effect-response framework that characterizes traits by how they predict species effects on their ecosystems or responses to environmental stressors. We then used cytochrome oxidase one sequences from the same specimens to generate a phylogeny and tested evolutionary tempo and mode of the traits. We found strong phylogenetic signal in, and correlations among, morphological ground beetle traits. These results indicate that, for these species, beetle body shape trait evolution is constrained, and phylogenetic inertia is a stronger driver of beetle traits than (recent) environmental responses. Strong correlations among effect and response traits suggest that future environmental drivers are likely to affect both ecological composition and functioning in these beetles.

evolutionary biology↗

Transmission of one predicts another: Apathogenic proxies for transmission dynamics of a fatal virus

Identifying drivers of transmission prior to an epidemic--especially of an emerging pathogen--is a formidable challenge for proactive disease management efforts. We tested a novel approach in the Florida panther, hypothesizing that apathogenic feline immunodeficiency virus (FIV) transmission could predict transmission dynamics for pathogenic feline leukemia virus (FeLV). We derived a transmission network using FIV whole genome sequences, and used exponential random graph models to determine drivers structuring this network. We used these drivers to predict FeLV transmission pathways among panthers and compared predicted outbreak dynamics against empirical FeLV outbreak data. FIV transmission was primarily driven by panther age class and distances between panther home range centroids. Prospective FIV-based modeling predicted FeLV dynamics at least as well as simpler, often retrospective approaches, with evidence that FIV-based predictions captured the spatial structuring of the observed FeLV outbreak. Our finding that an apathogenic agent can predict transmission of an analogously transmitted pathogen is an innovative approach that warrants testing in other host-pathogen systems to determine generalizability. Use of such apathogenic agents holds promise for improving predictions of pathogen transmission in novel host populations, and could thereby provide new strategies for proactive pathogen management in human and animal systems.

ecology↗

Emerging phylogenetic structure of the SARS-CoV-2 pandemic

Since spilling over into humans, SARS-CoV-2 has rapidly spread across the globe, accumulating significant genetic diversity. The structure of this genetic diversity, and whether it reveals epidemiological insights, are fundamental questions for understanding the evolutionary trajectory of this virus. Here we use a recently developed phylodynamic approach to uncover phylogenetic structures underlying the SARS-CoV-2 pandemic. We find support for three SARS-CoV-2 lineages co-circulating, each with significantly different demographic dynamics concordant with known epidemiological factors. For example, Lineage C emerged in Europe with a high growth rate in late February, just prior to the exponential increase in cases in several European countries. Mutations that characterize Lineage C in particular are non-synonymous and occur in functionally important gene regions responsible for viral replication and cell entry. Even though Lineages A and B had distinct demographic patterns, they were much more difficult to distinguish. Continuous application of phylogenetic approaches to track the evolutionary epidemiology of SARS-CoV-2 lineages will be increasingly important to validate the efficacy of control efforts and monitor significant evolutionary events in the future.

genetics↗

Host relatedness and landscape connectivity shape pathogen spread in a large secretive carnivore

Urban expansion can fundamentally alter wildlife movement and gene flow, but how urbanization alters pathogen spread is poorly understood. Here we combine high resolution host and viral genomic data with landscape variables to examine the context of viral spread in puma from two contrasting regions: one bounded by the wildland urban interface (WUI) and one unbounded with minimal anthropogenic development. We found landscape variables and host gene flow explained significant amounts of variation of feline immunodeficiency virus (FIV) spread in the WUI, but not in the unbounded region. The most important predictors of viral spread also differed; host spatial proximity, host relatedness, and mountain ranges played a role in FIV spread in the WUI, whereas unpaved roads were more important in the unbounded region. Our research demonstrates how anthropogenic landscapes can alter pathogen spread, providing a more nuanced understanding of host-pathogen relationships to inform disease ecology in free-ranging species.

ecology↗

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

O_LIMicrobial communities are increasingly recognised as crucial for animal health. However, our understanding of how microbial communities are structured across wildlife populations is poor. Mechanisms such as interspecific associations are important in structuring free-living communities, but we still lack an understanding of how important interspecific associations are in structuring gut microbial communities in comparison to other factors such as host characteristics or spatial proximity of hosts.\nC_LIO_LIHere we ask how gut microbial communities are structured in a population of North American moose (Alces alces). We identify key microbial interspecific associations within the moose gut and quantify how important they are relative to key host characteristics, such as body condition, for predicting microbial community composition.\nC_LIO_LIWe sampled gut microbial communities from 55 moose in a population experiencing decline due to a myriad of factors, including pathogens and malnutrition. We examined microbial community dynamics in this population utilizing novel graphical network models that can explicitly incorporate spatial information.\nC_LIO_LIWe found that interspecific associations were the most important mechanism structuring gut microbial communities in moose and detected both positive and negative associations. Models only accounting for associations between microbes had higher predictive value compared to models including moose sex, evidence of previous pathogen exposure, or body condition. Adding spatial information on moose location further strengthened our model and allowed us to predict microbe occurrences with [~]90% accuracy.\nC_LIO_LICollectively, our results suggest that microbial interspecific associations coupled with host spatial proximity are vital in shaping infra communities in a large herbivore. In this case, previous pathogen exposure and moose body condition were not as important in predicting gut microbial community composition. The approach applied here can be used to quantify interspecific associations and gain a more nuanced understanding of the spatial and host factors shaping microbial communities in non-model hosts.\nC_LI

ecology↗

Chronic infections can shape epidemic exposure: Pathogen co-occurrence networks in the Serengeti lions

Pathogens are embedded in a complex network of microparasites that can collectively or individually alter disease dynamics and outcomes. Chronic pathogens, for example, can either facilitate or compete with subsequent pathogens thereby exacerbating morbidity and mortality. Pathogen interactions are ubiquitous in nature, but poorly understood, particularly in wild populations. We report here on ten years of serological and molecular data in African lions, leveraging comprehensive demographic and behavioral data to utilize pathogen networks to test if chronic infections shape infection by acute pathogens. We combine network and community ecology approaches to assess broad network structure and characterize associations between pathogens across spatial and temporal scales. We found significant non-random structure in the lion-pathogen co-occurrence network and identified potential facilitative and competitive interactions between acute and chronic pathogens. Our results provide a novel insight for untangling the complex associations underlying pathogen co-occurrence networks.

ecology↗