SEARCH · bioRxiv Science

Results for “ecology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3Linked to original sources

bioRxiv2023

Emergent Ecological Patterns and Modelling of Gut Microbiomes in Health and in Disease

Recent advancements in next-generation sequencing have revolutionized our understanding of the human microbiome. Despite this progress, challenges persist in comprehending the microbiomes influence on disease, hindered by technical complexities in species classification, abundance estimation, and data compositionality. At the same time, recently the existence of macroecological laws describing the variation and diversity in microbial communities irrespective of their environment has been proposed using 16s data and explained by a simple phenomenological model of population dynamics. We here investigate the relationship between dysbiosis, i.e. in unhealthy individuals there are deviations from the "regular" composition of the gut microbial community, and the existence of macro-ecological emergent law in microbial communities. We first quantitatively reconstruct these patterns at the species level using shotgun data, offering a more biologically interpretable approach, and addressing the consequences of sampling effects and false positives on ecological patterns. We then ask if such patterns can discriminate between healthy and unhealthy cohorts. Concomitantly, we evaluate the efficacy of different population models, which incorporate sampling and different ecological and statistical principles (e.g., the Taylors law and environmental noise) to describe such patterns. A critical aspect of our analysis is understanding the relationship between model parameters, which have clear ecological interpretations, and the state of the gut microbiome, thereby enabling the generation of synthetic compositional data that distinctively represent healthy and unhealthy individuals. Our approach, grounded in theoretical ecology and statistical physics, allows for a robust comparison of these models with empirical data, enhancing our understanding of the strengths and limitations of simple microbial models of population dynamics. Author summaryIn this study, we explore emerging ecological properties in gut microbiomes. Our aim here is to determine whether these patterns can be informative of the gut microbiome (healthy or diseased) and unveil essential ingredients driving its population dynamics. Leveraging on phenomenological models of species abundance fluctuations and metagenomics data, we highlight the pivotal role of Taylors law, a straightforward mathematical relation, in constructing theoretical models for the human gut microbiome. We thus explore such a general theoretical framework for investigating microbiome composition and show that not all ecological patterns are informative to characterize its states, while few are (e.g., species diversity). Eventually, thanks to the ecological interpretability of the inferred models parameters, our analysis provides insights into the role of environmental fluctuations and carrying capacities of the gut microbiomes in both health and disease. This study offers valuable knowledge, bridging theoretical concepts with practical implications for human health.

ecology↗

bioRxiv2024

TwinEco: A Unified Framework for Dynamic Data-Driven Digital Twins in Ecology

1.A Digital Twin (DT) is a virtual replica of a physical object or process that is continuously updated at a certain frequency and can steer change on the physical system, enabling a seamless integration of observation, understanding, and action. Although initially applied primarily in industry, DT is emerging as a powerful tool in ecology, offering new possibilities for dynamic simulations of change in the biosphere. However, since DTs are relatively new in this field, there is currently no standard framework to guide their conceptualisation and development. Thus, DTs in ecological applications are already experiencing fragmentation in software concepts and design philosophies, leading to incompatibilities across DT implementations. This fragmentation risks undermining the progress and potential of the DT concept in ecology. A unifying framework, such as TwinEco, can address these discrepancies and establish a cohesive foundation for the effective adoption and integration of DTs across ecological domains. TwinEco is a modular framework designed to aid and harmonise ecologists efforts to build DTs. In doing so, TwinEco focuses on three major design goals: O_LIModularity, flexibility, and interoperability of DTs facilitated through distinct "components" nested within DT "layers". C_LIO_LIDynamic modeling of ecological processes and states that evolve over time. C_LIO_LILinking ecological modelling to downstream actions or decisions made on the ecological object or process of study. C_LI TwinEcos architecture builds upon the feedback loops and state management strategies introduced in the Dynamic Data-Driven Application Systems (DDDAS) paradigm, which has already inspired many DTs across scientific domains. We also discuss the usefulness and ease-of-use of TwinEco by demonstrating its applicability to computational case studies and suggesting future recommendations to the community of data infrastructure builders and modellers in regards to open considerations. By introducing a shared terminology and emphasising model-data fusion, TwinEco highlights the importance of a unified framework to avoid fragmentation in the burgeoning field of ecological digital twinning.

ecology↗

bioRxiv2018

Categorized analysis of forest ecological values in the China’s conversion cropland to forest program

Background\n\nThe Chinas Conversion Cropland to Forest Program (CCFP) is one of the large state ecological construction programs. Up to now, the program has effectively improved the ecological environment and produced large ecological benefit. However, there were also some problems in its implementation process, the program has been sometimes less effective than the expected.\n\nMethods\n\nBased on the data and the methods of State report on monitoring ecological effects in CCFP and the Chinese Forest Ecosystem Research Network (CFERN) in 2013, we analyzed the categorized forest ecological benefit value (B-V) s in the three forest restoration ways in different regions in China to provide references for CCFP construction.\n\nResults\n\nThe unit area B-Vs in CCFP varied between 35 000 RMBs.hm-2.a-1 and 100 000 RMBs.hm-2.a-1. Water conservation B-V and species conservation B-V were the two largest constituents, nutrient accumulation B-V was the least in all the categorized B-Vs on regional and unit area scale. The rank of restoration ways on average unit area total B-Vs was-- hillside forest conservation > returning cropland to forest > afforestation on suitable barren hills and wasteland in CCFP. Among the categorized B-Vs, some pairs were positively correlated with each other and some were negatively correlative. The correlation coefficients and some regression equations were given in the text and the attached Fig.s.\n\nConclusions\n\nWater conservation B-V was the highest and nutrient accumulation B-V was the lowest whether on regional or unit area scale in CCFP.\n\nForest ecological B-Vs varied in different forest restoration ways and different regions in CCFP. The hillside forest conservation restoration way and the water conservation B-V should be paid more attention in Chinas future forest restoration. We suggest that suitable forest restoration ways should be selective according to the regional specific and ecological targets.\n\nThere were correlations among the categorized B-Vs, and the correlations varied with different forest restoration ways in CCFP. Knowing about the correlations could clarify the targeted restoration ways according to the goal of ecological benefit.

ecology↗

bioRxiv2018

On the prevalence of uninformative parameters in statistical models applying model selection in applied ecology

Research in applied ecology provides scientific evidence to guide conservation policy and management. Applied ecology is becoming increasingly quantitative and model selection via information criteria has become a common statistical modeling approach. Unfortunately, parameters that contain little to no useful information are commonly presented and interpreted as important in applied ecology. I review the concept of an uninformative parameter in model selection using information criteria and perform a literature review to measure the prevalence of uninformative parameters in model selection studies applying Akaikes Information Criterion (AIC) in 2014 in four of the top journals in applied ecology (Biological Conservation, Conservation Biology, Ecological Applications, Journal of Applied Ecology). Twenty-one percent of studies I reviewed applied AIC metrics. Many (31.5 %) of the studies applying AIC metrics in the four applied ecology journals I reviewed had or were very likely to have uninformative parameters in a model set. In addition, more than 40 % of studies reviewed had insufficient information to assess the presence or absence of uninformative parameters in a model set. Given the prevalence of studies likely to have uninformative parameters or with insufficient information to assess parameter status (71.5 %), I surmise that much of the policy recommendations based on applied ecology research may not be supported by the data analysis. I provide warning signals and a decision tree to help reduce the prevalence of uninformative parameters in studies applying model selection with information criteria. The four warning signals and decision tree should assist authors, reviewers, and editors to screen for uninformative parameters in studies applying model selection with information criteria. In the end, careful thinking at every step of the scientific process and greater reporting standards are required to detect uninformative parameters in studies adopting an information criteria approach.

ecology↗

bioRxiv2019

Copulas reveal complex and informative dependencies propagating throughout ecology

All branches of ecology study relationships among and between environmental and biological variables. However, standard approaches to studying such relationships, based on correlation and regression, provide only a small slice of the complex information contained in the relationships. Other statistical approaches exist that provide a complete description of relationships between variables, based on the concept of the copula; they are applied in finance, neuroscience and other fields, but rarely in ecology. We here explore the concepts that underpin copulas and examine the potential for those concepts to improve our understanding of ecology. We find that informative copula structure in dependencies between variables is common across all the environmental, species-trait, phenological, population, community, and ecosystem functioning datasets we considered. Many datasets exhibited asymmetric tail associations, whereby two variables were more strongly related in their left compared to right tails, or vice versa. We describe mechanisms by which observed copula structure and asymmetric tail associations can arise in ecological data, including a Moran-like effect whereby dependence structures between environmental variables are inherited by ecological variables; and asymmetric or nonlinear influences of environments on ecological variables, such as under Liebigs law of the minimum. We also describe consequences of copula structure for ecological phenomena, including impacts on extinction risk, Taylors law, and the stability through time of ecosystem services. By documenting the importance of a complete description of dependence between variables, advancing conceptual frameworks, and demonstrating a powerful approach, we aim to encourage widespread use of copulas in ecology, which we believe can benefit the discipline.

ecology↗

bioRxiv2019

Ecological and dietary differences between Ugandan chimpanzee communities with possible implications on tool use

Some East African chimpanzee (Pan troglodytes schweinfurthii) communities, such as the Sonso chimpanzees, display an unusually limited range of tool-use, but it remains unclear whether this is due to ecological and/or cultural factors. Information on ecological conditions and the diet of the Sonso chimpanzees in relation to neighbouring communities is needed. Here, we studied three adjacent communities in Budongo Forest (Sonso, Waibira, and Kamira), and the presumed core area of an undescribed community (Mwera), in the neighbouring Bugoma Forest. Through line-transects, we investigated (i) whether there were differences in food diversity and abundance between the communities home ranges; (ii) whether the home ranges differed in abundance of sticks and insect nests; and (iii) whether Sonso and Mwera chimpanzees differed in their diet (using faecal samples). Across communities, Sonso had the richest food availability and the lowest insect nest abundance. However, food availability in Mwera, Bugoma, was richer than Budongo communities that neighbour the Sonso territory, suggesting that there may be variation within Budongo. Data from faecal samples replicated our direct observations of food availability suggesting that Sonso chimpanzees had a broader diet than Mwera chimpanzees. This difference in foods availability may partially explain the Sonso chimpanzees lack of stick-tool-use, and low levels of insectivory. The tool repertoire of the other communities is currently unknown; however, we make predictions based on our ecological data. More detailed knowledge of small-scale variation in ecology within and between forest habitats may be important to advancing our understanding of the drivers of tool-use.\n\nSIGNIFICANCE STATEMENT - HIGHLIGHTED STUDENT PAPERTo advance our knowledge of the role of ecological factors in the emergence of tool use in chimpanzees, a nuanced understanding of the ecological conditions different chimpanzee communities experience is needed. We studied four Ugandan chimpanzee communities in two forests. One of these communities, Sonso, in the Budongo Forest, is well-known for its restricted range of tool types, including a total absence of stick use. Food diversity and abundance were highest, and stick tool use opportunities (abundance of sticks and insect nests) were lowest for the core-habitat of the Sonso chimpanzees in contrast to the other communities. We argue that ecological factors play a role in their unusual pattern of tool use, and make predictions about the expected types of tool use in the other communities based on their ecology. Thus, our study provides information that may help advance our understanding of how tool use arises under varied socioecological circumstances.

ecology↗

bioRxiv2026

The topology of ecological drift

Ecological drift, the random fluctuation of abundance in communities, can drastically affect the possibility of coexistence. However, ecological drift has mostly been considered at the macro-ecological scale, whereas its potential contribution to short-term ecological dynamics remains underexplored. Here, we propose a stage-structured ecological graph theory (ssEcoGT) to include complex life cycles and multiple ecological interactions to study the topology of ecological drift. ssEcoGT enables rigorous exploration of how topology of a community can affect the possibility of coexistence between two species. Using ssEcoGT, it is possible to compare the behavior of a range of models - e.g., random graphs, random graphs with intraguild predation, and random graphs with rewiring - against a complete graph of the same size. Thus, ssEcoGT provides a new tool to explore the interplay between ecological drift, competition, and stage-specific interactions.

ecology↗

bioRxiv2026

Complex interplay of biomechanics and ecology influenced crab claw morphology evolution

True crabs (Brachyura) are among the most iconic marine arthropods, representing noteworthy examples of morphological and ecological disparity. A striking feature of brachyurans are their anterior pincer-like appendages: chelipeds. These structures showcase a large diversity of morphologies that reflect ecology and overall multifunctionality. Yet, a comprehensive assessment of appendage functional morphology within phylogenetic and ecological trait contexts has never been attempted. By combining 3D geometric morphometrics, finite element analyses, multilocus molecular phylogeny, and ecological trait data for 80 crab species, including three fossil forms, we unveil a complex evolutionary history for crab chelipeds. Despite extreme shape diversity amongst chelipeds, stress distributions are very similar across taxa and hint a many-to-one pattern. High concentrations of chelipeds within constrained morphospace regions associated with peak pinch forces illustrates that brachyuran morphologies optimised for shell crushing may have arisen in the Cretaceous. Deviations from this morphospace highlight the diversification of non-shell-crushing life modes and the influence of sexual selection on appendages. Neither cheliped shape nor pinch force show phylogenetic signal. Together these results indicate that the evolution of cheliped shape is closely associated with, and inferred to have been strongly influenced by, crab ecology, biomechanical needs and sexual selection. SIGNIFICANCE STATEMENTChelipeds, the pincer-like claws of crabs, are among the most morphologically diverse appendages within Arthropoda, yet the evolutionary forces driving this diversity remain poorly understood. By integrating 3D geometric morphometrics, biomechanical modelling, molecular phylogeny, and ecological data across 80 crab species including fossil forms, we demonstrate that cheliped morphology is driven by ecology, biomechanical demands, and sexual selection rather than phylogenetic relatedness. The multifunctionality of these structures produces strong evidence for many-to-one mapping of form to function. Morphologies optimised for durophagy appear to have originated in the Cretaceous, with subsequent diversification into manipulative and sexually selected forms from a morphologically flexible foundation. These findings demonstrate that cheliped diversity reflects a complex interplay between ecological specialisation, biomechanical optimisation, and sexual selection across Brachyura.

ecology↗

bioRxiv2026

Ecological context shapes the interpretation of biodiversity intactness metrics

Developing biodiversity metrics that are both operational for decision-making and ecologically meaningful remains challenging. Mean Species Abundance (MSA) is widely used to quantify biodiversity intactness in applications including biodiversity scenario modeling, spatial assessment, policy and planning, and life cycle assessment (LCA). MSA compares species abundance under disturbed conditions with their abundance under a reference condition, but the pressure-impact relationships used to calculate it are generalized across studies and may not adequately represent variation among ecological contexts or taxonomic groups. This is particularly relevant when MSA is transferred across regions or used to support comparisons and environmental decision-making. We compiled biodiversity data from 7,064 forest fragments containing 21,761 species of arthropods, amphibians, birds, mammals, squamates, and plants across 11 biomes worldwide. We evaluated how MSA relates to broader ecological outcomes, including local and regional species richness and ecosystem productivity, and whether these relationships vary across ecological contexts (vegetation condition, landscape structure, and biome) and taxonomic groups. MSA was positively associated with local species richness and ecosystem productivity across all sites, but these associations weakened, disappeared, or reversed depending on ecological context and taxonomic group. For example, the MSA-productivity association held in only five of 11 biomes, and the MSA-regional richness association was negative in temperate conifer and boreal forests but positive in four other biomes. We propose a simple decision guide linking assessment goals, contextual evaluation, and interpretation to help identify when MSA can be used directly, when ecological context should guide its interpretation, and when complementary ecological information is needed. These findings may extend to other biodiversity metrics that compare impacted conditions with reference states and apply generalized impact relationships across ecological contexts and taxonomic groups.

ecology↗

bioRxiv2021

Ecological outcomes of hybridization vary extensively in Catostomus fishes

Hybridization has been studied extensively to learn about speciation and mechanisms of reproductive isolation, but increasingly we recognize that hybridization outcomes vary geo-graphically and can depend on the environment. At the same time, hybridization can reshape biotic interactions in an ecosystem, leading to ecological shifts where hybridization occurs. Identifying how hybrid individuals function ecologically would link evolutionary outcomes of hybridization to ecological consequences, but relatively few studies have focused on ecological traits of hybrids. We described the feeding ecology of several Catostomus fish species and their hybrids by using stable isotopes ({delta}13C and{delta} 15N) as a proxy for diet and habitat use, and compared two native species, an introduced species, and three interspecific hybrid crosses. We replicated this comparison spatially, including hybrids and parental species from seven rivers in the Upper Colorado River basin where parental species co-occur and the opportunity for hybridization exists. Although relationships between native species in isotopic space varied, individual native species did not fully overlap in isotopic space in any river sampled, suggesting little overlap of resource use between these historically sympatric species. The introduced species overlapped with one or both native species in every river, suggesting similar resource use and potential for competition. Hybrids occupied intermediate, matching, or more extreme (transgressive) isotopic space relative to parental species, and were isotopically variable within and among rivers. We suggest that ecological outcomes of hybridization, like genomic outcomes of hybridization, are likely to vary across locations where a pair of species hybridizes. This variation implies that hybridization might have large unpredictable, idiosyncratic ecological effects on fish assemblages where hybrids occur. Although we found little evidence that hybrids are at a disadvantage ecologically--there were no significant declines in body condition relative to parental species--it is nevertheless possible that abiotic or biotic attributes of a river might constrain the range of interspecific hybrids that are successful, thus contributing to variation in hybridization outcomes across rivers.

evolutionary biology↗

bioRxiv2025

Ecological inference from isolated vertebrae: Evaluating functional signal across the carnivoran spine

Understanding the ecological adaptations of extinct species is a central goal in vertebrate palaeontology, but is often limited by the incomplete nature of the fossil record. While skulls and limb bones have traditionally been emphasized in functional and ecological reconstructions, vertebrae are frequently overlooked. While isolated vertebrae are among the most commonly preserved postcranial elements, they are rarely found as complete vertebral columns, raising the question of whether isolated elements alone can yield meaningful ecological information. In this study, we assess the potential of vertebral morphology to predict two key ecological traits, running speed and hunting mode, using three-dimensional geometric morphometrics across ten presacral vertebrae from a broad sample of extant carnivorans. We evaluate the predictive power of individual vertebrae, regional groupings (cervical, thoracic, lumbar), and multi-element combinations. Our results show that certain vertebrae retain strong ecological signals on their own, especially the first thoracic and lumbar elements. However, combining multiple vertebrae often dilutes ecological signal, likely due to their differing functional roles along the axial column. This highlights the importance of treating vertebral regions independently and suggests that single, strategically informative vertebrae may outperform multi-element approaches in some contexts. We apply this framework to the extinct dire wolf (Canis dirus) and find contrasting signals along the spine, the first thoracic and lumbar vertebrae suggest adaptations for faster locomotion, while some cervical vertebrae indicate an intermediate running speed. This mosaic supports the idea that C. dirus occupied a complex ecological niche involving both active predation and scavenging. These findings underscore the power of vertebral morphology for ecological inference in fossil taxa, particularly when remains are fragmentary, and argue for a more nuanced use of isolated axial elements in reconstructing extinct carnivoran behaviour.

paleontology↗

bioRxiv2026

Cross-ploidy hybridisation in Alpine woodrushes is associated with ecological additivity and scale-dependent niche divergence

O_LIHybridisation and whole-genome duplication (WGD) are widespread in plants, yet their ecological consequences remain challenging to predict. In allopolyploids, where both processes coincide, ecological divergence is typically evaluated against a null hypothesis of ecological additivity. However, this hypothesis has not been tested explicitly in the context of cross-ploidy hybridisation. C_LIO_LIWe assessed ecological additivity following cross-ploidy hybridisation in the Alpine woodrush Luzula alpina across multiple spatial resolutions. Integrating genomic data, environmental niche modelling, vegetation releves, and morphometric analyses, we characterised population structure and quantified ecological and morphological differentiation between the hybrid and its parental species. C_LIO_LIGenomic and morphometric evidence confirmed the hybrid origin of L. alpina. Patterns of niche evolution varied with spatial resolution. Climatic and edaphic data supported ecological additivity, whereas plot-level vegetation data revealed subtle but significant niche divergence accompanied by shifts in associated plant community composition. Postglacial population histories further suggest long-term persistence of hybrid and parental lineages in distinct refugia followed by differential recolonisation of the Alps. C_LIO_LIOur results indicate that cross-ploidy hybridisation in Alpine Luzula is predominantly associated with niche stability rather than pronounced ecological divergence. Importantly, the detection of divergence beyond ecological additivity depends on the spatial resolution of environmental data. C_LI

plant biology↗

bioRxiv2017

Stability and critical transitions in mutualistic ecological systems

Successful conservation of complex ecosystems, their function and associated services, requires deep understanding of their underlying dynamics and potential instabilities. While the study of ecological dynamics is a mature and diverse field, the lack of a general model that uses basic ecological parameters to predict system-level behaviour has allowed unresolved contradictions to persist. Here, we provide a general model of a mutualistic ecological community and show for the first time how the conditions for instability, the nature of ecological collapse, and potential early-warning signals, can be derived from the basic ecological parameters. We also resolve open questions concerning effects of interaction heterogeneity on both resilience and abundance, and discuss their potential trade-off in real systems. This framework provides a basis for rich investigations of ecological system dynamics, and can be generalised across many ecological contexts.

ecology↗

bioRxiv2017

Ecological Network Metrics: Opportunities For Synthesis

Network ecology provides a systems basis for approaching ecological questions, such as factors that influence biological diversity, the role of particular species or particular traits in structuring ecosystems, and long-term ecological dynamics (e.g. stability). Whereas the introduction of network theory has enabled ecologists to quantify not only the degree, but also the architecture of ecological complexity, these advances have come at the cost of introducing new challenges, including new theoretical concepts and metrics, and increased data complexity and computational intensity. Synthesizing recent developments in the network ecology literature, we point to several potential solutions to these issues: integrating network metrics and their terminology across sub-disciplines; benchmarking new network algorithms and models to increase mechanistic understanding; and improving tools for sharing ecological network research, in particular \"model\" data provenance, to increase the reproducibility of network models and analyses. We propose that applying these solutions will aid in synthesizing ecological subdisciplines and allied fields by improving the accessibility of network methods and models.

ecology↗

bioRxiv2020

Environmental biases in the study of ecological networks at the planetary scale

Ecological networks are increasingly studied at large spatial scales, expanding their focus from a conceptual tool for community ecology into one that also adresses questions in biogeography and macroecology. This effort is supported by increased access to standardized information on ecological networks, in the form of openly accessible databases. Yet, there has been no systematic evaluation of the fitness for purpose of these data to explore synthesis questions at very large spatial scales. In particular, because the sampling of ecological networks is a difficult task, they are likely to not have a good representation of the diversity of Earths bioclimatic conditions, likely to be spatially aggregated, and therefore unlikely to achieve broad representativeness. In this paper, we analyze over 1300 ecological networks in the mangal.io database, and discuss their coverage of biomes, and the geographic areas in which there is a deficit of data on ecological networks. Taken together, our results suggest that while some information about the global structure of ecological networks is available, it remains fragmented over space, with further differences by types of eco-logical interactions. This causes great concerns both for our ability to transfer knowledge from one region to the next, but also to forecast the structural change in networks under climate change.

ecology↗

bioRxiv2020

A preliminary ecological profile of Kyasanur Forest disease virus hosts among the mammalian wildlife of the Western Ghats, India

Kyasanur Forest disease (KFD) is one of Indias severe arboviruses capable of causing prolonged debilitating disease. It has been expanding beyond its historical endemic locus at an alarming rate over the last two decades. The natural nidus of this zoonosis is located in the monsoon rainforest of the Western Ghats, India, which is one of the worlds most important biodiversity hotspots. Definitive reservoir hosts for KFD virus (KFDV) have yet to be delineated, and thus much of the infection ecology of this virus, and its consequent transmission dynamics, remains uncertain. Given its unique biogeographical context, identifying ecological parameters of KFDV relevant to the virus epidemiology has been complex and challenging. The challenge has been exacerbated by diminished research efforts in wildlife surveillance over the last two decades, coinciding with the expansion of the range of KFD across the region. The current investigation sought to define a preliminary ecological profile of KFDV hosts based on their life history and feeding traits to aid in re-establishing targeted wildlife surveillance and to discern those ecological traits of wildlife hosts that may improve our understanding of KFD epidemiology. The importance of fast-living among KFDV hosts was of special interest with respect to the latter aim. We compared mammalian traits between host and non-host species using general additive models and phylogenetic generalised linear models. This study found that both body mass and forest forage were strongly associated with mammalian host infection status, but that reproductive life history traits were not. These findings will help in structuring ecologically based wildlife surveillance and field investigations, while also helping to parameterise novel epidemiological models of zoonotic infection risk that incorporate species functional traits in a region where biogeography, landscape ecology, and community ecology manifest extraordinary complexity, particularly under growing anthropogenic pressure.

ecology↗

bioRxiv2020

The rise of disease ecology

Micro- and macroparasites are a leading cause of mortality for humans, animals, and plants, and there is great need to understand their origins, transmission dynamics, and impacts. Disease ecology formed as an interdisciplinary field in the 1970s to fill this need and has recently rapidly grown in size and influence. Because interdisciplinary fields integrate diverse scientific expertise and training experiences, understanding their composition and research priorities is often difficult. Here, for the first time, we quantify the composition and educational experiences of a subset of disease ecology practitioners and identify topical trends in published research. We combined a large survey of self-declared disease ecologists with a literature synthesis involving machine-learning topic detection of over 18,500 disease ecology research articles. The number of graduate degrees earned by disease ecology practitioners has grown dramatically since the early 2000s. Similar to other science fields, we show that practitioners in disease ecology have diversified in the last decade in terms of gender identity and institution, with weaker diversification in race and ethnicity. Topic detection analysis revealed how the frequency of publications on certain topics have declined (e.g., HIV, serology), increased (e.g., the dilution effect, infectious disease in bats), remained relatively common (e.g., malaria ecology, influenza, vaccine research and development), or have consistently remained relatively infrequent (e.g., theoretical models, field experiments). Other topics, such as climate change, superspreading, emerging infectious diseases, and network analyses, have recently come to prominence. This study helps identify the major themes of disease ecology and demonstrates how publication frequency corresponds to emergent health and environmental threats. More broadly, our approach provides a framework to examine the composition and publication trends of other major research fields that cross traditional disciplinary boundaries.

ecology↗

bioRxiv2020

NetworkExtinction: an R package to explore the propagation of extinctions through complex ecological networks

O_LIEarths biosphere is currently undergoing drastic reorganisation as a consequence of the sixth mass extinction brought on by the Anthropocene. Impacts of local and regional extirpation of species have been demonstrated to propagate through the complex interaction networks they are part of, subsequently leading to secondary extinctions, exacerbating biodiversity loss. Contemporary ecological theory has developed several measures to analyse the structure and robustness of ecological networks under biodiversity loss. However, a toolbox for direct simulation and quantification of extinction cascades and the creation of novel interactions (i.e. rewiring) remains absent. C_LIO_LIHere, we present NetworkExtinction - a novel R package which we have developed to explore the propagation of species extinctions sequences through ecological networks as well as quantify the effects of rewiring potential in response to primary species extinctions. With NetworkExtinction we have integrated ecological theory and computational simulations to develop functionality with which users may analyze and visualize the structure and robustness of ecological networks. The core functions introduced with NetworkExtinction focus on simulations of sequential primary extinctions and associated secondary extinctions while allowing for user-specified secondary extinction thresholds and realisation of rewiring potential. C_LIO_LIWith the package NetworkExtinction, users can estimate the robustness of ecological networks after performing species extinction routines based on several algorithms. Moreover, users can compare the number of simulated secondary extinctions against a null model of random extinctions. In-built visualizations enable graphing topological indices calculated by the deletion sequence functions after each simulation step. Finally, the user can define the degree distribution of the network by fitting different common distributions. Here, we illustrate the use of the package and its outputs by analyzing a Chilean coastal marine food web. C_LIO_LINetworkExtinction is a compact and easy-to-use R package with which users can quantify changes in ecological network structure in response to different patterns of species loss, thresholds, and rewiring potential. Therefore, this package is particularly useful to evaluate ecosystem responses to anthropogenic and environmental perturbations that produce non-random species extinctions. C_LI

ecology↗