Combining Phylogenetic and Occurrence Information for Risk Assessment of Pest and Pathogen Interactions with Host Plants

Abstract

Phytosanitary agencies conduct plant biosecurity activities, including early detection of potential introduction pathways, to improve control and eradication of pest and pathogen incursions. For such actions, analytical tools based on solid scientific knowledge regarding plant-pest or pathogen relationships for pest risk assessment are needed. Recent evidence indicating that closely related species share a higher chance of becoming infected or attacked by pests has allowed the identification of taxa with different degrees of vulnerability. Here, we use information readily available online about pest-host interactions and their geographic distributions, in combination with host phylogenetic reconstructions, to estimate a pest-host interaction (in some cases infection) index in geographic space as a more comprehensive, spatially explicit tool for risk assessment. We demonstrate this protocol using phylogenetic relationships for 20 beetle species and 235 host plant genera: first, we estimate the probability of a host sharing pests, and second, we project the index in geographic space. Overall, the predictions allow identification of the pest-host interaction type (e.g., generalist or specialist), which is largely determined by both host range and phylogenetic constraints. Furthermore, the results can be valuable in terms of identifying hotspots where pests and vulnerable hosts interact. This knowledge is useful for anticipating biological invasions or spreading of disease. We suggest that our understanding of biotic interactions will improve after combining information from multiple dimensions of biodiversity at multiple scales (e.g., phylogenetic signal and host-vector-pathogen geographic distribution).

Phylogenetic signals in pest abundance and distribution range of spider mites

“…Several studies have introduced phylogenetic information into pest risk assessments (Gilbert et al 2012(Gilbert et al , 2015. Because closely related plants generally share similar pests (Gilbert and Webb 2007;Futuyma and Agrawal 2009), phylogenetic information can be used to predict which plant species are likely to be susceptible to a particular pest (De Vienne et al 2009;Gilbert et al 2012;Robles-Fernández and Lira-Noriega 2017). However, such information was not sufficient to evaluate whether pest damage on a given host or in a novel region is severe or benign (Gilbert et al 2012).…”

“…Species extinction risk is often not randomly spread across phylogeny (Hampe and Petit 2005;Fritz and Purvis 2010;Arbetman et al 2017), indicating that phylogeny could be useful in predicting the fate of species (Willis et al 2008;Purvis 2008;Gallagher et al 2015). In risk assessments, phylogenetic information has also been used to predict which plant species are likely to be susceptible to a particular pest (De Vienne et al 2009;Gilbert et al 2012;Robles-Fernández and Lira-Noriega 2017), because closely-related plants tend to have similar traits (e.g. plant defensive chemicals) and host similar pests when compared to evolutionarily distant plant species (Gilbert and Webb 2007).…”

American Mammals Susceptibility to Dengue According to Geographical, Environmental, and Phylogenetic Distances

“…The use of analytical statistical tools can take advantage of knowledge on host breadth, environmental variables, geographic distributions, and host phylogenies to develop predictive frameworks to generate geographical assessments of infection risk, which can be applied to either host assemblages or a focal host species by either a group of pathogens or by a specific pathogen of interest [e.g., ( 30 )]. Thus, our aim is to predict sylvatic host assemblages of DENV in the Americas via machine learning statistical protocols, in order to create preventive frameworks useful for health agencies (e.g., CDC) that can aid to forecast the probability or risk of potential hazards ( 31 ).…”

Phylogenetic signals in pest abundance and distribution range of spider mites

“…Species extinction risk is often not randomly spread across phylogeny [3], indicating that phylogeny could be useful in predicting the fate of species [19, 52]. In risk assessments, phylogenetic information has also been used to predict which plant species are likely to be susceptible to a particular pest [23, 55], because closely-related plants tend to have similar traits (e.g. plant defensive chemicals) and host similar pests when compared to evolutionarily distant plant species [24].…”