Nicholas Clark

Nicholas Clark
The University of Queensland | UQ · School of Veterinary Science

BSc, MAppSci, PhD

About

75
Publications
42,853
Reads
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1,307
Citations
Citations since 2016
63 Research Items
1259 Citations
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Introduction
Quantitative ecologist and ARC DECRA Fellow working at the nexus between molecular ecology, host-pathogen interactions and spatio-temporal modelling. My work focuses on exploring new ways to (1) understand how natural communities are formed and (2) predict how they will change over time. Twitter: @nj_clark Orcid ID: orcid.org/0000-0001-7131-3301 Lab website: http://www.spatialepilab.com/
Additional affiliations
June 2016 - June 2016
The University of Queensland
Position
  • PostDoc Position
February 2012 - May 2016
Griffith University
Position
  • PhD Student
February 2010 - February 2011
James Cook University
Position
  • Master's Student

Publications

Publications (75)
Article
Full-text available
[Background] Spillover of parasites at the domestic animal - wildlife interface is a pervasive threat to animal health. Cat and dog fleas (Ctenocephalides felis and C. canis) are among the world’s most invasive and economically important ectoparasites. Although both species are presumed to infest a diversity of host species across the globe, knowle...
Article
Full-text available
Aim Characterizing macroecological patterns in biodiversity is key to improve our understanding of community assembly. Global biodiversity for many taxa follows a latitudinal gradient, with increased diversity in tropical latitudes. Less is known about global parasite biodiversity, inhibiting our ability to predict how global change will impact par...
Article
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Inferring interactions between co‐occurring species is key to identify processes governing community assembly. Incorporating interspecific interactions in predictive models is common in ecology, yet most methods do not adequately account for indirect interactions (where an interaction between two species is masked by their shared interactions with...
Article
Host specificity encompasses the range and diversity of host species that a parasite is capable of infecting and is considered a crucial measure of a parasite’s potential to shift hosts and trigger disease emergence. Yet empirical studies rarely consider that regional observations only reflect a parasite’s ‘realized’ host range under particular con...
Article
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Marine ecosystems are under increasing threat from warming waters. Winter warming is occurring at a faster rate than summer warming for ecosystems around the world, but most studies focus on the summer. Here, we show that winter warming could affect coastal fish community compositions in the Mediterranean Sea using a model that captures how biotic...
Article
Introduction That foot infections are predominately polymicrobial has long been recognized, but it is not clear if the various species co-occur randomly or in patterns. We sought non-random species co-occurrence patterns that might help better predict prognosis or guide antimicrobial selection. Methods We analyzed tissue (bone, skin, and other sof...
Article
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Generalised additive models (GAMs) are increasingly popular tools for estimating smooth nonlinear relationships between predictors and response variables. GAMs are particularly relevant in ecology for representing hierarchical functions for discrete responses that encompass complex features including zero inflation, truncation and uneven sampling....
Article
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Q fever, caused by the bacterium Coxiella burnetii, is an important zoonotic disease worldwide. Australia has one of the highest reported incidences and seroprevalence of Q fever, and communities in the state of Queensland are at highest risk of exposure. Despite Australia’s Q fever vaccination programs, the number of reported Q fever cases has rem...
Article
Point 1: Species Distribution Models (SDMs) are vital tools for predicting species occurrences and are used in many practical tasks including conservation and biodiversity management. However, the expanding minefield of SDM methodologies makes it difficult to select the most reliable method for large co‐occurrence datasets, particularly when time c...
Article
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Canine rabies poses a significant risk to humans and animals in Nigeria. However, the lack of reliable tools to evaluate the performance of existing canine rabies control programs to inform public health policy decisions poses a severe obstacle. We obtained canine rabies surveillance data from the National Veterinary Research Institute (NVRI) and s...
Preprint
Full-text available
Generalised Additive Models (GAMs) are increasingly popular for describing smooth nonlinear relationships between predictors and response variables. GAMs are particularly relevant in ecology for representing hierarchical functions for discrete responses that encompass complex features including zero-inflation, bounding and uneven sampling. However,...
Article
Full-text available
Tick paralysis resulting from bites from Ixodes holocyclus and I. cornuatus is one of the leading causes of emergency veterinary admissions for companion animals in Australia, often resulting in death if left untreated. Availability of timely information on periods of increased risk can help modulate behaviors that reduce exposures to ticks and imp...
Conference Paper
Dog mediated rabies remains a significant public health risk in Nigeria. We obtained rabies surveillance data from the National Veterinary Research Institute (NVRI), supplemented this information with published literature from Nigeria, and retrieved environmental and sociodemographic variables that might explain canine rabies at the Local Gover...
Article
The occurrence and clinical significance of the protozoal parasite reported as Hepatozoon tachyglossi in wild short‐beaked echidnas (Tachyglossis aculeatus) have long been uncertain, as has its potential as a prognostic indicator. This retrospective survey of free‐ranging short‐beaked echidnas admitted to a wildlife hospital used morphological evid...
Article
Full-text available
Aim: Macroecological analyses provide valuable insights into factors that influence how parasites are distributed across space and among hosts. Amid large uncertainties that arise when generalizing from local and regional findings, hierarchical approaches applied to global datasets are required to determine whether drivers of parasite infection pat...
Article
Tick paralysis is an uncommon cause of neuromuscular paralysis affecting 0.12% of wild birds presented to Currumbin Wildlife Sanctuary, Queensland, with a strong seasonal predilection towards spring and summer. Clinical signs and progression of paralysis showed similarities to companion animals and were consistent across 20 species. Tick location,...
Article
We introduce a new R package ‘MrIML’ (‘Mister iml’; Multi-response Interpretable Machine Learning). MrIML provides a powerful and interpretable framework that enables users to harness recent advances in machine learning to quantify multi-locus genomic relationships, to identify loci of interest for future landscape genetics studies, and to gain new...
Article
Full-text available
Integration of community ecology with disease biology is viewed as a promising avenue for uncovering determinants of pathogen diversity, and for predicting disease risks. Plant-infecting viruses represent a vastly underestimated component of biodiversity with potentially important ecological and evolutionary roles. We performed hierarchal spatial a...
Preprint
Full-text available
Integration of community ecology with disease biology is viewed as a promising avenue for uncovering determinants of pathogen diversity, and for predicting disease risks. Plant-infecting viruses represent a vastly underestimated component of biodiversity with potentially important ecological and evolutionary roles. We performed hierarchal spatial a...
Article
Full-text available
Canine companion animals can carry a number of zoonotic parasites which can adversely impact both human and animal health. Previous studies in Australia indicated that while parasitic infections in dogs are still common and there is variability in the awareness and perception of zoonotic risks among pet owners, the likely contribution of sociodemog...
Preprint
Full-text available
We introduce a new R package ‘MrIML’ (Multi-response Interpretable Machine Learning). MrIML provides a powerful and interpretable framework that enables users to harness recent advances in machine learning to map multi-locus genomic relationships, to identify loci of interest for future landscape genetics studies and to gain new insights into adapt...
Article
Q fever is a zoonotic disease caused by the intracellular bacterium, Coxiella burnetii. Its primary mode of transmission is by inhalation of aerosols originating from infected animals and contaminated environments. The organism has a very low infective dose, can persist in the environment for long periods of time and large outbreaks fuelled by wind...
Article
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Identifying robust environmental predictors of infection probability is central to forecasting and mitigating the ongoing impacts of climate change on vector‐borne disease threats. We applied phylogenetic hierarchical models to a dataset of 2,171 Western Palearctic individual birds from 47 species to determine how climate and landscape variation in...
Article
Objective To determine the current porcine circovirus type 2 (PCV2) genotypes circulating in pigs in Queensland (QLD). Methods The PCV2 infection status of pigs was determined by real‐time PCR testing of 210 lymph nodes and 30 serum samples derived from 45 QLD farms. PCV2‐positive samples from 22 pigs from 15 farms were subjected to conventional p...
Article
Full-text available
Q fever, caused by the zoonotic bacterium Coxiella burnetii, is a globally distributed emerging infectious disease. Livestock are the most important zoonotic transmission sources, yet infection in people without livestock exposure is common. Identifying potential exposure pathways is necessary to design effective interventions and aid outbreak prev...
Article
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Background: Schistosomiasis and infection by soil-transmitted helminths are some of the world's most prevalent neglected tropical diseases. Infection by more than one parasite (co-infection) is common and can contribute to clinical morbidity in children. Geostatistical analyses of parasite infection data are key for developing mass drug administra...
Article
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1.Geographic variation in environmental conditions as well as host traits that promote parasite transmission may impact infection rates and community assembly of vector transmitted parasites. 2.Identifying the ecological, environmental, and historical determinants of parasite distributions and diversity is therefore necessary to understand disease...
Article
Microbial 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 interspeci...
Article
Full-text available
Background Schistosomiasis is a neglected tropical disease caused by Schistosoma parasites. Intervention relies on identifying high-risk regions, yet rapid Schistosoma diagnostics (Kato-Katz stool assays (KK) and circulating cathodic antigen urine assays (CCA)) yield different prevalence estimates. We mapped S. mansoni prevalence and delineated at-...
Article
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Within host-parasite communities, viral co-circulation and co-infections of hosts are the norm, yet studies of significant emerging zoonoses tend to focus on a single parasite species within the host. Using a multiplexed paramyxovirus bead-based PCR on urine samples from Australian flying foxes, we show that multi-viral shedding from flying fox pop...
Article
1.Social network analysis has been postulated as a tool to study potential pathogen transmission in wildlife but is resource intensive to quantify. Networks based on bacterial genotypes have been proposed as a cost‐effective method for estimating social or transmission network based on the assumption that individuals in close contact will share com...
Article
Full-text available
Soil-transmitted helminth (STH) infections are globally distributed intestinal parasite infections caused by Ascaris lumbricoides, Trichuris trichiura, and hookworms (Ancylostoma duodenale and Necator americanus). STH infection constitutes a major public health threat, with heavy burdens observed in many of the world’s tropical and subtropical regi...
Article
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Parasites with low host specificity (e.g. infecting a large diversity of host species) are of special interest in disease ecology, as they are likely more capable of circumventing ecological or evolutionary barriers to infect new hosts than are specialist parasites. Yet for many parasites, host specificity is not fixed and can vary in response to e...
Article
Full-text available
The cat flea (Ctenocephalides felis) is the most common parasite of domestic cats and dogs worldwide. Due to the morphological ambiguity of C. felis and a lack of — particularly largescale — phylogenetic data, we do not know whether global C. felis populations are morphologically and genetically conserved, or whether human-mediated migration of dom...
Data
The development of methods to detect how a species’ occurrence probability covaries with the occurrences of other species (e.g. co-occurrence) is a booming and somewhat divisive area of statistical ecology. Many authors (including, sadly, myself) have jumped the gun when interpreting co-occurrence patterns by grandiosely stating that they reflect '...
Preprint
Full-text available
Microbial 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 interspeci...
Experiment Findings
A key aim of this research is to understand how multi-host parasites are spread, both across geographical regions and across potential host species. This is especially relevant since the way humans convert natural habitats into production landscapes, in addition to wildlife trades and the spread of invasive species, are increasing contact patterns...
Article
Full-text available
Background: Q fever is a zoonotic disease caused by Coxiella burnetii. This bacterium survives harsh conditions and attaches to dust, suggesting environmental dispersal is a risk factor for outbreaks. Spatial epidemiology studies collating evidence on Q fever geographical contamination gradients are needed, as human cases without occupational expos...
Article
Full-text available
Changes in species distributions open novel parasite transmission routes at the human–wildlife interface, yet the strength of biotic and biogeographical factors that prevent or facilitate parasite host shifting are not well understood. We investigated global patterns of helminth parasite (Nematoda, Cestoda, Trematoda) sharing between mammalian wild...
Article
Tracing the temporal dynamics of pathogens is crucial for developing strategies to detect and limit disease emergence. Canine parvovirus (CPV-2) is an enteric virus causing morbidity and mortality in dogs around the globe. Previous work in Australia reported that the majority of cases were associated with the CPV-2a subtype, an unexpected finding s...
Article
Full-text available
Identifying barriers that govern parasite community assembly and parasite invasion risk is critical to understand how shifting host ranges impact disease emergence. We studied regional variation in the phylogenetic compositions of bird species and their blood parasites (Plasmodium and Haemoproteus spp.) to identify barriers that shape parasite comm...
Article
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Is the origin of gibbon ape leukemia virus (GALV) human after all? When GALV was discovered and found to cause neoplastic disease in gibbons, it stimulated a great deal of research including investigations into the origins of this virus. A number of publications have suggested that the GALV progenitor was a retrovirus present in one of several spec...
Article
The range of hosts a pathogen infects (host specificity) is a key element of disease risk that may be influenced by both shared phylogenetic history and shared ecological attributes of prospective hosts. Phylospecificity indices quantify host specificity in terms of host relatedness, but can fail to capture ecological attributes that increase susce...
Article
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Migratory birds make decisions about how far to travel based on cost-benefit trade-offs. However, in many cases the net effect of these trade-offs is unclear. We sought to address this question by measuring feather corticosterone (CORTf), leucocyte profile, avian malaria parasite prevalence and estimating fueling rates in three spatially segregated...
Article
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Linking morphological studies with molecular phylogeny is important to understanding cryptic speciation and the evolution of host-parasite relationships. Haemosporidian parasites of the Australo-Papuan bird family Artamidae are relatively unstudied. Only one parasite species from the subfamily Cracticinae has been described, and this was based sole...
Article
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Experimental work increasingly suggests that non-random pathogen associations can affect the spread or severity of disease. Yet due to difficulties distinguishing and interpreting co-infections, evidence for the presence and directionality of pathogen co-occurrences in wildlife is rudimentary. We provide empirical evidence for pathogen co-occurrenc...
Article
Full-text available
Pathogen exposure has been suggested as one of the factors shaping the myriad of migration strategies observed in nature. Two hypotheses relate migration strategies to pathogen infection: the “avoiding the tropics hypothesis” predicts that pathogen prevalence and transmission increase with dec