Machine learning algorithms for the evaluation of risk by tick-borne pathogens in Europe

BACKGROUND

Tick-borne pathogens pose a major threat to human health worldwide. Understanding the epidemiology of tick-borne diseases to reduce their impact on human health requires models covering large geographic areas and considering both the abiotic traits that affect tick presence, as well as the vertebrates used as hosts, vegetation, and land use. Herein, we integrated the public information available for Europe regarding the variables that may affect habitat suitability for ticks and hosts and tested five machine learning algorithms (MLA) for predicting the distribution of four prominent tick species across Europe.

MATERIALS AND METHODS

A grid of cells 20 km in diameter was prepared to cover the entire territory, containing data on vegetation, points of water, habitat fragmentation, forest density, grass extension, or imperviousness, with information on temperature and water deficit. The distribution of the hosts (162 species) was modelled and included in the dataset. We used five MLA, namely, Random Forest, Neural Networks, Naive Bayes, Gradient Boosting, and AdaBoost, trained with reliable coordinates for Ixodes ricinus, Dermacentor reticulatus, Dermacentor marginatus, and Hyalomma marginatum in Europe.

RESULTS

Both Random Forest and Gradient Boosting best predicted ticks and host environmental niches. Our results demonstrate that MLA can identify trait-matching combinations of environmental niches. The inclusion of land cover and land use variables has a superior capacity for predicting areas suitable for ticks, compared to classic methods based on the use of climate data alone.

CONCLUSIONS

Flexible MLA-driven models may offer several advantages over traditional models. We anticipate that these results may be extrapolated to other regions and combinations of tick-vertebrates. These results highlight the potential of MLA for inference in ecology and provide a background for the evolution of a completely automatized tool to calculate the seasonality of ticks for early warning systems aimed at preventing tick-borne diseases.

Biodiversity in changing environments: An external-driver internal-topology framework to guide intervention

Accompanying the climate crisis is the more enigmatic biodiversity crisis. Rapid reorganization of biodiversity due to global environmental change has defied prediction and tested the basic tenets of conservation and restoration. Conceptual and practical innovation is needed to support decision making in the face of these unprecedented shifts. Critical questions include: How can we generalize biodiversity change at the community level? When are systems able to reorganize and maintain integrity, and when does abiotic change result in collapse or restructuring? How does this understanding provide a template to guide when and how to intervene in conservation and restoration? To this end, we frame changes in community organization as the modulation of external abiotic drivers on the internal topology of species interactions, using plant-plant interactions in terrestrial communities as a starting point. We then explore how this framing can help translate available data on species abundance and trait distributions to corresponding decisions in management. Given the expectation that community response and reorganization are highly complex, the external-driver internal-topology (EDIT) framework offers a way to capture general patterns of biodiversity that can help guide resilience and adaptation in changing environments.

A successional shift enhances stability in ant symbiont communities

Throughout succession, communities undergo structural shifts, which can alter the relative abundances of species and how they interact. It is frequently asserted that these alterations beget stability, i.e. that succession selects for communities better able to resist perturbations. Yet, whether and how alterations of network structure affect stability during succession in complex communities is rarely studied in natural ecosystems. Here, we explore how network attributes influence stability of different successional stages of a natural network: symbiotic arthropod communities forming food webs inside red wood ant nests. We determined the abundance of 16 functional groups within the symbiont community across 51 host nests in the beginning and end stages of succession. Nest age was the main driver of the compositional shifts: symbiont communities in old nests contained more even species abundance distributions and a greater proportion of specialists. Based on the abundance data, we reconstructed interaction matrices and food webs of the symbiont community for each nest. We showed that the enhanced community evenness in old nests leads to an augmented food web stability in all but the largest symbiont communities. Overall, this study demonstrates that succession begets stability in a natural ecological network by making the community more even.

Higher-order species interactions cause time-dependent niche and fitness differences: Experimental evidence in plant-feeding arthropods

Species interact in different ways, including competition, facilitation and predation. These interactions can be non-linear or higher order and may depend on time or species densities. Although these higher-order interactions are virtually ubiquitous, they remain poorly understood, as they are challenging both theoretically and empirically. We propose to adapt niche and fitness differences from modern coexistence theory and apply them to species interactions over time. As such, they may not merely inform about coexistence, but provide a deeper understanding of how species interactions change. Here, we investigated how the exploitation of a biotic resource (plant) by phytophagous arthropods affects their interactions. We performed monoculture and competition experiments to fit a generalized additive mixed model to the empirical data, which allowed us to calculate niche and fitness differences. We found that species switch between different types of interactions over time, including intra- and interspecific facilitation, and strong and weak competition.

Trophic tug-of-war: Coexistence mechanisms within and across trophic levels

Ecological communities encompass rich diversity across multiple trophic levels. While modern coexistence theory has been widely applied to understand community assembly, its traditional formalism only allows assembly within a single trophic level. Here, using an expanded definition of niche and fitness differences applicable to multitrophic communities, we study how diversity within and across trophic levels affects species coexistence. If each trophic level is analysed separately, both lower- and higher trophic levels are governed by the same coexistence mechanisms. In contrast, if the multitrophic community is analysed as a whole, different trophic levels are governed by different coexistence mechanisms: coexistence at lower trophic levels is predominantly limited by fitness differences, whereas coexistence at higher trophic levels is predominantly limited by niche differences. This dichotomy in coexistence mechanisms is supported by theoretical derivations, simulations of phenomenological and trait-based models, and a case study of a primeval forest ecosystem. Our work provides a general and testable prediction of coexistence mechanism operating in multitrophic communities.

Bridging theory and experiments of priority effects

Priority effects play a key role in structuring natural communities, but considerable confusion remains about how they affect different ecological systems. Synthesizing previous studies, we show that this confusion arises because the mechanisms driving priority and the temporal scale at which they operate differ among studies, leading to divergent outcomes in species interactions and biodiversity patterns. We suggest grouping priority effects into two functional categories based on their mechanisms: frequency-dependent priority effects that arise from positive frequency dependence, and trait-dependent priority effects that arise from time-dependent changes in interacting traits. Through easy quantification of these categories from experiments, we can construct community models representing diverse biological mechanisms and interactions with priority effects, therefore better predicting their consequences across ecosystems.

Building modern coexistence theory from the ground up: The role of community assembly

Modern coexistence theory (MCT) is one of the leading methods to understand species coexistence. It uses invasion growth rates-the average, per-capita growth rate of a rare species-to identify when and why species coexist. Despite significant advances in dissecting coexistence mechanisms when coexistence occurs, MCT relies on a 'mutual invasibility' condition designed for two-species communities but poorly defined for species-rich communities. Here, we review well-known issues with this component of MCT and propose a solution based on recent mathematical advances. We propose a clear framework for expanding MCT to species-rich communities and for understanding invasion resistance as well as coexistence, especially for communities that could not be analysed with MCT so far. Using two data-driven community models from the literature, we illustrate the utility of our framework and highlight the opportunities for bridging the fields of community assembly and species coexistence.

Restoration ecology through the lens of coexistence theory

Advances in restoration ecology are needed to guide ecological restoration in a variable and changing world. Coexistence theory provides a framework for how variability in environmental conditions and species interactions affects species success. Here, we conceptually link coexistence theory and restoration ecology. First, including low-density growth rates (LDGRs), a classic metric of coexistence, can improve abundance-based restoration goals, because abundances are sensitive to initial treatments and ongoing variability. Second, growth-rate partitioning, developed to identify coexistence mechanisms, can improve restoration practice by informing site selection and indicating necessary interventions (e.g., site amelioration or competitor removal). Finally, coexistence methods can improve restoration assessment, because initial growth rates indicate trajectories, average growth rates measure success, and growth partitioning highlights interventions needed in future.

Mechanistic Models of Trophic Interactions: Opportunities for Species Richness and Challenges for Modern Coexistence Theory

AbstractMany potential mechanisms promote species coexistence, but we know little about their relative importance. To compare multiple mechanisms, we modeled a two-trophic planktonic food web based on mechanistic species interactions and empirically measured species traits. We simulated thousands of possible communities under realistic and altered interaction strengths to assess the relative importance of three potential drivers of phytoplankton and zooplankton species richness: resource-mediated coexistence mechanisms, predator-prey interactions, and trait trade-offs. Next, we computed niche and fitness differences of competing zooplankton to obtain a deeper understanding of how these mechanisms determine species richness. We found that predator-prey interactions were the most important driver of phytoplankton and zooplankton species richness and that large zooplankton fitness differences were associated with low species richness, but zooplankton niche differences were not associated with species richness. However, for many communities we could not apply modern coexistence theory to compute niche and fitness differences of zooplankton because of conceptual issues with the invasion growth rates arising from trophic interactions. We therefore need to expand modern coexistence theory to fully investigate multitrophic-level communities.

Specific sequence of arrival promotes coexistence via spatial niche pre-emption by the weak competitor

Historical contingency, such as the order of species arrival, can modify competitive outcomes via niche modification or pre-emption. However, how these mechanisms ultimately modify stabilising niche and average fitness differences remains largely unknown. By experimentally assembling two congeneric spider mite species feeding on tomato plants during two generations, we show that order of arrival affects species' competitive ability and changes the outcome of competition. Contrary to expectations, order of arrival did not cause positive frequency dependent priority effects. Instead, coexistence was predicted when the inferior competitor (Tetranychus urticae) arrived first. In that case, T. urticae colonised the preferred feeding stratum (leaves) of T. evansi leading to spatial niche pre-emption, which equalised fitness and reduced niche differences, driving community assembly to a close-to-neutrality scenario. Our study demonstrates how the order of species arrival and the spatial context of competitive interactions may jointly determine whether species can coexist.

Disentangling key species interactions in diverse and heterogeneous communities: A Bayesian sparse modelling approach

Modelling species interactions in diverse communities traditionally requires a prohibitively large number of species-interaction coefficients, especially when considering environmental dependence of parameters. We implemented Bayesian variable selection via sparsity-inducing priors on non-linear species abundance models to determine which species interactions should be retained and which can be represented as an average heterospecific interaction term, reducing the number of model parameters. We evaluated model performance using simulated communities, computing out-of-sample predictive accuracy and parameter recovery across different input sample sizes. We applied our method to a diverse empirical community, allowing us to disentangle the direct role of environmental gradients on species' intrinsic growth rates from indirect effects via competitive interactions. We also identified a few neighbouring species from the diverse community that had non-generic interactions with our focal species. This sparse modelling approach facilitates exploration of species interactions in diverse communities while maintaining a manageable number of parameters.

More than What Meets the Eye: Differential Spatiotemporal Distribution of Cryptic Intertidal Bangiales

Morphologically similar but genetically distinct species have been termed cryptic and most have been assumed to be ecologically similar. However, if these species co-occur at a certain spatial scale, some niche differences at finer scales should be expected to allow for coexistence. Here, we demonstrate the existence of a disjointed distribution of cryptic bladed Bangiales along spatial (intertidal elevations) and temporal (seasons) environmental gradients. Bladed Bangiales were identified and quantified across four intertidal elevations and four seasons for one year, at five rocky intertidal sites (between 39° S and 43° S) in southern Chile. Species determination was based on partial sequences of the mitochondrial cytochrome c oxidase 1 (COI) gene amplification. To assess species gross morphology, thallus shape, color, and maximum length and width were recorded. Hundreds of organisms were classified into nine Bangiales species belonging to three genera (i.e., Fuscifolium, Porphyra, and Pyropia), including five frequent (>97% of specimens) and four infrequent species. All species, except for Pyropia saldanhae, had been previously reported along the coasts of Chile. The thallus shape and color were very variable, and a large overlap of the maximum width and length supported the cryptic status of these species. Multivariate analyses showed that the main variable affecting species composition was intertidal elevation. Species such as Py. orbicularis were more abundant in low and mid intertidal zones, while others, such as Po. mumfordii and Po. sp. FIH, were principally observed in high and spray elevations. Despite all numerically dominant species being present all year long, a slight effect of seasonal variation on species composition was also detected. These results strongly support the existence of spatial niche partitioning in cryptic Bangiales along the Chilean rocky intertidal zone.