Towards an eco‐phylogenetic framework for infectious disease ecology

Fountain-Jones, Nicholas M.; Pearse, William D.; Escobar, Luis E.; Alba-Casals, Ana; Carver, Scott; Davies, T. Jonathan; Kraberger, Simona; Papeş, Monica; Vandegrift, Kurt J.; Worsley‐Tonks, Katherine E. L.; Craft, Meggan E.

doi:10.1111/brv.12380

Cited by 72 publications

(74 citation statements)

References 167 publications

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“…The niche similarity tests offer biological realism to the different models by giving access to a broader perspective that support the idea of phylogenetic niche conservatism among the Leptospira lineages studied (Escobar, Qiao, Phelps, Wagner, & Larkin, ; Martinez‐Meyer, Diaz‐Porras, Peterson, & Yanez‐Arenas, ; Yañez‐Arenas, Peterson, Mokondoko, Rojas‐Soto, & Martínez‐Meyer, ). The importance and significance of the use of these similarity tests at serovar level relies on the fact that disease transmission is the product of complex interactions that involves ecological, evolutionary and epidemiological processes (Fountain‐Jones et al, ; Galvani, ; Peterson, ).…”

Section: Discussionmentioning

confidence: 99%

Spatial distribution and spread potential of sixteenLeptospiraserovars in a subtropical region of Brazil

Jara

Escobar

Rodriges³

et al. 2019

Transbound Emerg Dis

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Leptospirosis is a bacterial disease that represents a major problem in animal and public health due to its high prevalence and widespread distribution. This zoonotic disease is most prevalent in tropical environments where conditions favour pathogen survival. The ecological preferences of Leptospira serovars are poorly understood, limiting our knowledge of where and when outbreaks can occur, which may result in misinformed prevention and control plans. While the disease can occur consistently in time and space in tropical regions, research on the ecology of leptospirosis remains limited in subtropical regions. This research gap regarding Leptospira ecology brings public and veterinary health problems, impacting local economies. To fill this gap of knowledge, we suggest to assess geographic and ecological features among Leptospira serovars in a subtropical area of Brazil where leptospirosis is endemic to (a) highlight environmental conditions that facilitate or limit Leptospira spread and survival and (b) reconstruct its geographic distribution. An ecological niche modelling framework was used to characterize and compare Leptospira serovars in both geographic and environmental space. Our results show that despite the geographic overlap exhibited by the different serovars assessed, we found ecological divergence among their occupied ecological niches. Ecological divergences were expressed as ranges of potential distributions and environmental conditions found suitably by serovar, Sejroe being the most asymmetric (<0.15). Most important predictors for the potential distribution of most serovars were soil pH (31.7%) and landscape temperature (24.2%). Identification of environmental preferences will allow epidemiologists to better infer the presence of a serovar based on the environmental characteristics of regions rather than inferences based solely on historical epidemiological records. Including geographic and ecological ranges of serovars also may help to forecast transmission potential of Leptospira in public health and the food animal practice.

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Section: Discussionmentioning

confidence: 99%

Spatial distribution and spread potential of sixteenLeptospiraserovars in a subtropical region of Brazil

Jara

Escobar

Rodriges³

et al. 2019

Transbound Emerg Dis

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“…Developing landscape resistance hypotheses for transmitted agents may be more difficult as their interactions with the landscape are often indirect, mediated by the ecology of hosts and vectors. Pathogen ecological niche models offer an empirical approach for constructing resistance surfaces based on ecological factors influencing pathogen prevalence (Escobar et al., ; Fountain‐Jones, Pearse et al., ), but these also may not adequately represent host/vector movements.…”

Section: Common Methodological Approaches In Landscape Genetics and Tmentioning

confidence: 99%

“…Other studies have investigated landscape genetic structure in multiple hosts of the same pathogens, identifying divergent dispersal patterns that could be integrated into studies of pathogen gene flow under such a framework (Rioux Paquette et al., ; Vander Wal et al., ). Approaches that consider whole ecological communities have recently been identified as necessary for advancing our understanding of pathogen dynamics (Fountain‐Jones, Pearse et al., ; Johnson, de Roode, & Fenton, ). Studies integrating multiple host and vector species into landscape genetic models of spread of infectious agents represent an important step towards such a paradigm.…”

Section: Emerging Concepts For the Landscape Genetics Of Infectious Amentioning

confidence: 99%

“…Phylogenetic approaches can reconstruct very recent epidemic histories, providing insights into particular transmission events and pathways that may be contextualized temporally and spatially (Corman et al., ; Faria et al., ; Carroll et al., ; Magee, Beard, Suchard, Lemey, & Scotch, ; Fountain‐Jones, Packer, et al., ; Fountain‐Jones, Pearse et al., ). The majority of such work has been conducted on RNA viruses owing to their small, rapidly mutating genomes, requiring relatively little sequencing effort to detect contemporary phylogenetic signals.…”

Section: Emerging Concepts For the Landscape Genetics Of Infectious Amentioning

confidence: 99%

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Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics

Kozakiewicz

Burridge

Funk

et al. 2018

Evolutionary Applications

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Landscape genetics has provided many insights into how heterogeneous landscape features drive processes influencing spatial genetic variation in free‐living organisms. This rapidly developing field has focused heavily on vertebrates, and expansion of this scope to the study of infectious diseases holds great potential for landscape geneticists and disease ecologists alike. The potential application of landscape genetics to infectious agents has garnered attention at formative stages in the development of landscape genetics, but systematic examination is lacking. We comprehensively review how landscape genetics is being used to better understand pathogen dynamics. We characterize the field and evaluate the types of questions addressed, approaches used and systems studied. We also review the now established landscape genetic methods and their realized and potential applications to disease ecology. Lastly, we identify emerging frontiers in the landscape genetic study of infectious agents, including recent phylogeographic approaches and frameworks for studying complex multihost and host‐vector systems. Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. Through this review, we convey how increasing awareness of the complementarity of landscape genetics and disease ecology among practitioners of each field promises to drive important cross‐disciplinary advances.

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“…Such factors may include broad physiological tolerances (large A H ) or increased transmissibility (M H ) between host populations with overlapping geographic ranges ( Figure 3C [36,75]). Furthermore, parasites may experience expansions in their occupied host breadth (H O ) following landscape alterations or shifts in their geographic distributions [75,78] (see Box 3 for applications).…”

Section: Niches In Host-spacementioning

confidence: 99%

An Ecological Framework for Modeling the Geography of Disease Transmission

Johnson

Escobar

Zambrana‐Torrelio

2019

Trends in Ecology & Evolution

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104

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Ecological niche modeling (ENM) is widely employed in ecology to predict species' potential geographic distributions in relation to their environmental constraints and is rapidly becoming the gold-standard method for disease risk mapping. However, given the biological complexity of disease systems, the traditional ENM framework requires reevaluation. We provide an overview of the application of ENM to disease systems and propose a theoretical framework based on the biological properties of both hosts and parasites to produce reliable outputs resembling disease system distributions. Additionally, we discuss the differences between biological considerations when implementing ENM for distributional ecology and epidemiology. This new framework will help the field of disease ecology and applications of biogeography in the epidemiology of infectious diseases. Challenges and Opportunities to Map Disease RiskThe recent rise of emerging infectious diseases (EIDs) (see Glossary) [1] has increased the burden of infectious diseases and negatively impacted the global economy [2][3][4][5]. Approximately 60% of emerging human diseases are caused by pathogenic parasites of animal origin (zoonoses), particularly wildlife [6]. As human activities intensify, contact with wildlife and exposure to novel parasites increase, potentially driving zoonotic disease emergence [1,7]. Given the threat that EIDs pose to human populations, understanding the underlying drivers of parasite geographic distribution and their spillover to humans is particularly relevant for epidemiologists, public-health practitioners, and policy makers [9].Ecological niche modeling (ENM) has proven useful to forecast the distribution of a vast number of organisms [10-13] and is increasingly employed to predict parasite distributions locally and globally [14][15][16][17]. Despite great strides made in the implementation of ENM to forecast complex biological phenomena such as disease systems [18], traditional frameworks may render biologically unrealistic predictions and thus must be revised, as we show in this review. We provide an overview of the current state of disease ENM and propose a framework based on the biological properties of both parasites and hosts to produce reliable outputs resembling disease systems distributions. Specifically, our theoretical framework: (i) addresses the selection of an appropriate modeling approach and highlights the importance of including biologically sound predictor variables; (ii) proposes the concept of a microscale parasitic niche defined by host traits to identify relevant parasite-host associations; and (iii) integrates traditional parasite ENM with the proposed microscale niche to better understand geographic distributions and improve fine-scale predictions of disease transmission risk. ENM and Biotic InteractionsENM estimates the distributions of species by linking their geographic occurrence with their environmental constraints, often utilizing correlative approaches (detailed explanations in [18]). Highlights

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Towards an eco‐phylogenetic framework for infectious disease ecology

Cited by 72 publications

References 167 publications

Spatial distribution and spread potential of sixteenLeptospiraserovars in a subtropical region of Brazil

Spatial distribution and spread potential of sixteenLeptospiraserovars in a subtropical region of Brazil

Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics

An Ecological Framework for Modeling the Geography of Disease Transmission

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