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Results for “ecology”

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bioRxiv2020

BEEM-Static: Accurate inference of ecological interactions from cross-sectional metagenomic data

MotivationThe structure and function of diverse microbial communities is underpinned by ecological interactions that remain uncharacterized. With rapid adoption of metagenomic sequencing for studying microbiomes, data-driven inference of microbial interactions based on abundance correlations is widely used, but with the drawback that ecological interpretations may not be possible. Leveraging cross-sectional metagenomic datasets for unravelling ecological structure in a scalable manner thus remains an open problem. MethodsWe present an expectation-maximization algorithm (BEEM-Static) that can be applied to cross-sectional datasets to infer interaction networks based on an ecological model (generalized Lotka-Volterra). The method exhibits robustness to violations in model assumptions by using statistical filters to identify and remove corresponding samples. ResultsBenchmarking against 10 state-of-the-art correlation based methods showed that BEEM-Static can infer presence and directionality of ecological interactions even with relative abundance data (AUC-ROC>0.85), a task that other methods struggle with (AUC-ROC<0.63). In addition, BEEM-Static can tolerate a high fraction of samples (up to 40%) being not at steady state or coming from an alternate model. Applying BEEM-Static to a large public dataset of human gut microbiomes (n=4,617) identified multiple stable equilibria that better reflect ecological enterotypes with distinct carrying capacities and interactions for key species. ConclusionBEEM-Static provides new opportunities for mining ecologically interpretable interactions and systems insights from the growing corpus of metagenomic data.

bioinformatics↗

bioRxiv2021

Quantifying the impact of ecological memory on the dynamics of interacting communities

Ecological memory refers to the influence of past events on the response of an ecosystem to exogenous or endogenous changes. Memory has been widely recognized as a key contributor to the dynamics of ecosystems and other complex systems, yet quantitative community models often ignore memory and its implications. Recent modeling studies have shown how interactions between community members can lead to the emergence of resilience and multistability under environmental perturbations. We demonstrate how memory can be introduced in such models using the framework of fractional calculus. We study how the outcomes of a well-characterized interaction model are affected by gradual increases in ecological memory under varying initial conditions, perturbations, and stochasticity. Our results highlight the implications of memory on several key aspects of community dynamics. In general, memory introduces inertia into the dynamics. This favors species coexistence under perturbation, enhances system resistance to state shifts, mitigates hysteresis, and can affect system resilience both ways depending on the time scale considered. Memory also promotes long transient dynamics, such as long-standing oscillations and delayed regime shifts, and contributes to the emergence and persistence of alternative stable states. Our study highlights the fundamental role of memory on ecological communities, and provides quantitative tools to introduce it in ecological models and analyse its impact under varying conditions. Author summaryAn ecosystem is said to exhibit ecological memory when its future states do not only depend on its current state but also on its initial state and trajectory. Memory may arise through various mechanisms as organisms adapt to their environment, modify it, and accumulate biotic and abiotic material. It may also emerge from phenotypic heterogeneity at the population level. Despite its commonness in nature, ecological memory and its potential influence on ecosystem dynamics have been so far overlooked in many applied contexts. Here, we use modeling to investigate how memory can influence the dynamics, composition, and stability landscape of ecological communities. We incorporate long-term memory effects into a multi-species model recently introduced to investigate alternative stable states in microbial communities. We assess the impact of memory on key aspects of model behavior and validate our findings using a model parameterized by empirical data from the human gut microbiota. Our approach for modeling memory and studying its implications has the potential to improve our understanding of microbial community dynamics and ultimately our ability to predict, manipulate, and experimentally design microbial ecosystems. It could also be applied more broadly in the study of systems composed of interacting components.

systems biology↗

bioRxiv2021

Model-checking ecological state-transition graphs

Model-checking is a methodology developed in computer science to automatically assess the dynamics of discrete systems, by checking if a system modelled as a state-transition graph satisfies a dynamical property written as a temporal logic formula. The dynamics of ecosystems have been drawn as state-transition graphs for more than a century, from state-and-transition models to assembly graphs. Thus, model-checking can provide insights into both empirical data and theoretical models, as long as they sum up into state-transition graphs. While model-checking proved to be a valuable tool in systems biology, it remains largely underused in ecology. Here we promote the adoption of the model-checking toolbox in ecology through its application to an illustrative example. We assessed the dynamics of a vegetation model inspired from state-and-transition models by model-checking Computation Tree Logic formulas built from a proposed catalogue of patterns. Model-checking encompasses a wide range of concepts and available software, mentioned in discussion, thus its implementation can be fitted to the specific features of the described system. In addition to the automated analysis of ecological state-transition graphs, we believe that defining ecological concepts with temporal logics could help clarifying and comparing them. Author summaryEcologists have drawn state-transition graphs representing the dynamics of ecosystems for more than a century. Model-checking is an automated method for the analysis of such graphs developed in computer science and acknowledged by a Turing award in 2007. Ecologists appear to be mostly unaware of model-checking despite its successes in systems biology to assess the dynamics of biological networks. We promote model-checking of ecological state-transition graphs through its application to an illustrative vegetation model. We exemplify the insights provided by model-checking by assessing management policies aiming to tackle savanna encroachment. We also provide a catalogue of patterns to help ecologists with the difficulty of formally expressing dynamical properties. We also discuss the wide range of model-checking concepts and available software, enabling to fit the specific features of the studied system, such as durations or probabilities. Model-checking can be applied to both empirical data and theoretical models, as long as they sum up into state-transition graphs. It provides automated and accurate answers to complex questions that could barely be analysed through human examination, if not impossible to answer this way. In addition to the automated analysis of ecological state-transition graphs, we believe that formally defining ecological concepts within the model-checking framework could help in clarifying and comparing them.

bioinformatics↗

bioRxiv2022

New forms of ecological knowledge acquisition for freshwater mussels' conservation

Freshwater mussels are of recognized importance for ecosystem functioning, for the provision of ecosystem services, and for human well-being. Whether people are more concerned about freshwater mussels has a large role to play in promoting and supporting political decisions that protect their habitat. A pilot study was performed in the Midwest of the United States to evaluate the awareness people have about freshwater mussels both native and non-native. Using semi-structured face-to-face interviews, I explore whether ecological knowledge is still in place in the community, and what the relationship is between knowledge, age and urbanization. Multinomial logistic regression has shown that population size and age class are significant predictors of ecological knowledge. Present results suggest that common channels of ecological knowledge transmission have been interrupted long ago. As a result, local ecological knowledge is being substituted by modern ecological knowledge. Nevertheless, new processes of ecological knowledge acquisition emerge. Under this scenario, future management prospects would rely on state institutions which are implementing alternative dissemination pathways in modern socio-ecological systems.

scientific communication and education↗

bioRxiv2022

A new Paleogene fossil and a new dataset for waterfowl (Aves: Anseriformes) clarify phylogeny, ecological evolution, and avian evolution at the K-Pg Boundary.

AbstractDespite making up one of the most ecologically diverse groups of living birds, comprising soaring, diving and giant flightless taxa, the evolutionary relationships and ecological evolution of Anseriformes (waterfowl) remain unresolved. Although Anseriformes have a comparatively rich, global Cretaceous and Paleogene fossil record, morphological datasets for this group that include extinct taxa report conflicting relationships for all known extinct taxa. Correct placement of extinct taxa is necessary to understand whether ancestral anseriform feeding ecology was more terrestrial or one of a set of diverse aquatic ecologies and to better understand avian evolution around the K-T boundary. Here, we present a new morphological dataset for Anseriformes that includes more extant and extinct taxa than any previous anseriform-focused dataset and describe a new anseriform species from the early Eocene Green River Formation of North America. The new taxon has a mediolaterally narrow bill which is not known in any previously described anseriform fossils other than portions of the pseudotoothed Pelagornithidae. The matrix created to assess the placement of this taxon comprises 41 taxa and 719 discrete morphological characters describing skeletal morphology, musculature, syringeal morphology, ecology, and behavior. We additionally combine the morphological dataset with published sequences using Bayesian methods and perform ancestral state reconstruction for ecological and behavioral characters. We recover the new Eocene taxon as a stem anseranatid across all analyses, and find that the new taxon represents a novel ecology within known Anseriformes and the Green River taxa. Results indicate that Anseriformes were likely ancestrally aquatic herbivores with rhamphothecal lamellae and provide insight into avian evolution during and following the K-Pg mass extinction.

evolutionary biology↗

bioRxiv2023

Carrion converging: Skull shape is predicted by feeding ecology in vultures

The link between skull shape and dietary ecology in birds at macroevolutionary scales has recently been called into question by analyses of 3D shape that reveal that cranial anatomy is mainly influenced by other factors such as allometry. It is still unknown whether this form-function disconnect also exists at smaller evolutionary scales, for example within specialized ecological guilds. Vultures are a diverse guild of 23 extant species in two families (Accipitridae and Cathartidae) that exhibit phenotypic convergence as a result of highly-specialized feeding ecology. Vultures are the only known obligate scavengers among vertebrates and are usually grouped together under this single dietary category, but within this specialized diet there are three distinct, species-specific feeding strategies termed ripper, gulper, and scrapper. We use three-dimensional geometric morphometrics to quantify the relative contributions of feeding ecology, allometry, and phylogeny on vulture skull shape, along with several non-vulture raptors of similar size, range and ecology. Families show clear separation in shape, but phylogenetic signal is comparatively weak (Kmult = 0.33). Taking into account the influence of phylogeny, skull shape is not significantly correlated with either skull size or feeding type, but there are examples of strong, significant convergence and parallel shape evolution across feeding groups. Furthermore, skull shape performs strongly in predicting feeding ecology in a phylogenetic discriminant function analysis. These findings highlight the importance of detailed assessment of feeding behavior in studies of ecomorphology, rather than broader dietary categories alone, and reveal that ecology can be readily inferred from form given appropriate information.

evolutionary biology↗

bioRxiv2023

The socio-spatial ecology of giant anteaters in the Brazilian Cerrado

Movement is a key component of an animals life history. While there are numerous factors that influence movement, there is an inherent link between a species social ecology and its movement ecology. Despite this inherent relationship, the socio-spatial ecology of many species remains unknown, hampering ecological theory and conservation alike. Here, we use fine-scale GPS location data and continuous-time stochastic processes to study the socio-spatial ecology of 23 giant anteaters (Myrmecophaga tridactyla) in the Brazilian Cerrado. We found that individuals occupied stable home ranges with a mean area of 5.45 km2 with males having significantly larger home ranges than females. The average amount of home-range overlap was low (0.20, n = 121 dyads), with no evidence that giant anteater home ranges were structured based on territorial, mate guarding, nor other social behaviour. We also identified a total of 2774 encounter events. Interestingly, both female-male and male-male dyads had significantly more encounters than female-female dyads, with two pronounced seasonal peaks in female-male encounters. Though encounters occurred frequently, associations between dyads were generally weak and there was little evidence of any correlated movement (mean amount of total correlation = 0.01). Collectively, these findings suggest giant anteaters are a solitary and largely asocial species that readily share space with conspecifics. Despite their present capacity to share space, the combined pressures of being condensed into smaller areas and decreased food availability due to increased pesticide use may see behavioural changes radiating throughout the population. Our study provides insight into heretofore unknown aspects of the socio-spatial ecology of this iconic, but understudied species, as well as crucial information for proactive area-based management. Ultimately, these findings contribute towards sustainable development while potentially maintaining the ecological integrity of giant anteaters and their habitats.

animal behavior and cognition↗

bioRxiv2024

Bacterial defenses and their trade-off with growth are not ubiquitous but depend on ecological contexts

Bacteriophages, also known as bacterial viruses, significantly influence microbial ecosystems, driving bacteria to evolve diverse antiviral defense mechanisms. This study explores the intricate relationship between bacterial defenses and growth rates across diverse ecological contexts. Our investigation reveals that bacteria lacking defenses exhibit prolonged doubling times. Integrating phylogenetic eigenvectors into the ecological feature matrix, we employed a phylogenetic random forest model to identify key ecological features influencing defense presence and abundance. Further phylogenetic regressions unveil nuanced dependencies of bacterial defenses on specific environmental factors, challenging assumptions of a universal defense system distribution and underscoring reliance on subtle ecological cues. Notably, symbiotic and endosymbiotic bacteria often exhibit reduced defense systems and negative correlations between defense system abundance and the minimal doubling time. Conversely, free-living and motile bacteria show significant positive correlations between minimal doubling time and defense system abundance. Moreover, we highlight the pivotal role of ecological variables like habitat specificity and nutrient availability in shaping bacterial growth rates and defense mechanisms. Our findings underscore the complexity of microbial interactions and stress the need to consider ecological context in understanding defense strategies. We propose that trade-offs between growth and defense are ubiquitous due to sporadically inefficient optimization of limited resources, particularly in populations with small effective sizes, where both mechanisms may weaken concurrently due to genetic drift. This challenges traditional notions of trade-offs and underscores the impact of ecological context on microbial strategies.

microbiology↗

bioRxiv2025

Ecological stoichiometry and life history theory, not the identity of genomic variants, predict rapid adaptation

SignificanceForecasting how populations adapt to changing environments is a central challenge in evolutionary biology. We tested the predictability of rapid adaptation by tracking both phenotypic and genomic trajectories of evolution in replicate outdoor populations of Drosophila melanogaster and comparing these data to predictions derived from life history theory, ecological stoichiometry, and genomic data. We found that life history theory and ecological stoichiometry forecasted the direction of phenotypic evolution, even with temporal changes in the direction of evolution. In contrast, genomic predictors were largely unable to forecast the SNPs or genes underlying adaptation. These results demonstrate the utility of ecological frameworks to provide general, but robust, forecasts of adaptation in complex environments. Determining the scale and scope of the predictability of evolution is fundamental to understanding biological processes and to managing biodiversity. Ecological frameworks, including life history theory and ecological stoichiometry, offer testable predictions about the direction of adaptation and trade-offs between traits in response to environmental change. Similarly, well-characterized molecular pathways, genotype-phenotype linkages, and prior evolutionary genomic studies could be predictive of the genomic architecture underlying adaptation. We tested whether ecological frameworks and evolutionary genomic data can be used to forecast rapid adaptation in replicated outdoor populations of Drosophila melanogaster evolving in response to natural seasonal fluctuations from summer to late fall. Life history theory predicted the observed pattern of adaptive tracking: in summer, reproductive output increased and stress tolerance decreased, while in fall, this direction reversed, with evolution of increased stress tolerance at the expense of reproduction. Stoichiometric phenotypic evolution was also predictable, with phosphorus and magnesium content, both linked to growth rate, and alkali metal, associated with maintaining homeostasis in response to thermal stress, showing rapid and parallel evolution indicative of adaptation. Temporal genomic data revealed a complex genomic architecture of temporal adaptation and the SNPs and genes involved in adaptation were largely unpredictable. These results demonstrate that ecological frameworks, more than genomic data, have utility in forecasting adaptation in complex and variable environments.

evolutionary biology↗

bioRxiv2017

Eco-evolutionary dynamics under limited dispersal: ecological inheritance, altruism within and spite between species

Understanding selection on ecological interactions that take place in dispersal-limited communities is an important challenge for ecology and evolutionary biology. The problem is that local demographic stochasticity generates eco-evolutionary dynamics that are too complicated to make tractable analytical investigations. Here, we circumvent this problem by approximating the selection gradient on a quantitative trait that influences local community dynamics, assuming that such dynamics are deterministic with a stable fixed point, but incorporating the kin selection effects arising from demographic stochasticity. Our approximation reveals that selection depends on how an individual expressing a trait-change influences: (1) its own fitness and the fitness of its current relatives; and (2) the fitness of its downstream relatives through modifications of local ecological conditions (i.e., through ecological inheritance). Mathematically, the effects of ecological inheritance on selection are captured by dispersal-limited versions of press-perturbations of community ecology. We use our approximation to investigate the evolution of helping within- and harming between-species when these behaviours influence demography. We find helping evolves more readily when competition is for material resources rather than space because then, the costs of kin competition are paid by downstream relatives. Similarly, harming between species evolves when it alleviates downstream relatives from inter-specific competition. Beyond these examples, our approximation can help better understand the influence of ecological inheritance on a variety of eco-evolutionary dynamics, from plant-pollinator to predator-prey coevolution.

evolutionary biology↗

bioRxiv2018

Spatial and ontogenetic variation in susceptibility to polarotactic ecological traps

Ecological traps occur when environmental cues become unreliable, causing an evolutionary mismatch between features of the environment and expected outcome that leads to suboptimal behavioural responses and, ultimately, reduced fitness. Ecological traps arise due to anthropogenic disturbance in the environment introducing novel elements that mimic those environmental cues. Therefore, ecological traps represent a strong selective pressure in areas where anthropogenic changes are frequent, such as cities. However, given the exposure to these traps over generations, localised adaptations to ecological traps might be expected in urban populations. Dragonflies and damselflies (Odonata) are one of the many taxa vulnerable to ecological traps: odonates use horizontally polarised light as a cue of suitable water bodies, although some artificial surfaces also reflect horizontally polarised light strongly, thus misleading odonates to oviposit preferentially on these unsuitable surfaces rather than in water. Here, we compare the behavioural response to horizontally polarised light between urban and rural populations of the odonate Ischnura elegans to test the potential for localised adaptations to ecological traps. Laboratory choice experiments were performed using field-caught adults from urban and rural areas, and individuals reared in controlled conditions to account for environmental variation and exposure to polarised light. We also studied the association between ontogeny and polarotaxis that has been suggested - but not empirically tested - by other studies. The results showed that field-caught rural individuals had a significantly stronger preference for horizontally polarised light compared to urban individuals, suggesting there is strong selection against polarotaxis in urban areas. However, individuals reared in controlled conditions showed no difference between urban and rural populations, suggesting that there has not yet been adaptation in urban odonates. Instead, adults developed a strong preference for horizontally polarised light with increasing age, showing that mature adults are more prone to ecological traps. Possible mechanisms driving this response are discussed.

evolutionary biology↗

bioRxiv2018

Animal virus ecology and evolution are shaped by the virus host-body infiltration and colonization pattern.

The current classification of animal viruses primarily relates to the virus molecular world, the genomic architecture and the corresponding host-cell infection cycle. This virus centered perspective does not make allowance for the precept that virus fitness hinges on the virus transmission success. Virus transmission reflects the infection-shedding-transmission dynamics and, with it, the organ system involvement and other, macroscopic dimensions of the host environment. This study examines the transmission ecology of the world main livestock viruses, 36 in total, belonging to eleven different families, and a mix of RNA, DNA and retroviruses. Viruses are virtually ranked in an outer- to inner-body fashion, based on the shifting organ system involvement and associated infection-shedding-transmission dynamics. As a next step, this ranking is disentangled with the aim to contrast two main host ecologies, poultry plus pig production and ruminant plus equine husbandry, as well as to create a distinction among the RNA, DNA and retroviruses, also ranked in an outer- to inner-body fashion. Spearman correlation reveals the matches among these various virus traits, as pertaining to the two host-ecologies, four infection-shedding-transmission related variables, and the three virus genomes. The collective results reveal the outer- to inner-body shifts in the interplay of host environment, virus-host interactions, and nature of the virus. Two opposing virus evolution pathways emerge, respectively for generalist type, outer-body and for specialist type, inner-body viruses. The ecological virus classification here presented is broadly consistent with the current virus classification system and offers the advantage of bringing substance and cohesion to the interrelationships among viruses and virus families.\n\nAuthor SummaryIt remains unknown how exactly viruses fit in the tree of life. Still, there is growing awareness that viruses as biological replicators are subjected to ecological sorting and so require a viable propagation strategy. In the current analysis I depart from the precept that virus fitness hinges on the virus transmission success. I examine the transmission ecologies of the world main livestock viruses, 36 in total, a collection of pathogens well described in terms of the organ system involvement, infection course, the extent of host damage, virus shedding profile, and virus transmission modes. The viruses are on this basis ranked in an outer- to inner-body fashion, virtually. As a next step, this ranking is disentangled with a view to contrast two main host ecologies, poultry plus pig production and ruminant plus equine husbandry, as well as to create a distinction among the RNA, DNA and retrovirus in the study. The matches among these various virus traits serve to establish the outer- to inner-body shifts in the interplay of host environment, virus-host interactions, and nature of the virus. Two opposing virus evolution pathways emerge, respectively for generalist type, outer-body and for specialist, inner-body viruses.

evolutionary biology↗

bioRxiv2019

Quantifying shape, integration, and ecology in avian pedal claws: comparing geometric morphometric and traditional metric approaches

Terrestrial tetrapods use their claws to interact with their environments in a plethora of ways. Birds in particular have developed a diversity of claw shapes since they are not bound to terrestrial locomotion and have heterogeneous body masses ranging several orders of magnitude. Numerous previous studies have hypothesized a connection between pedal claw shape and ecological mode in birds, but have generated conflicting results, spanning from clear ecological groupings based on claw shape to a complete overlap of ecological modes. These studies have relied on traditional morphometric arc measurements of keratinous sheaths and have variably accounted for likely confounding factors such as body mass and phylogenetic relatedness. To better address the hypothesized relationship between ecology and claw shape in birds, 580 radiographs were collected allowing visualization of the bony core and keratinous sheath shape spanning 21 avian orders. A new method was used to quantify claw shape using geometric morphometrics and was compared to results using traditional arc measurements. Neither traditional nor geometric morphometrics are capable of significantly separating bird claws into coarse ecological categories after integrating body size and phylogenetic relatedness. Further, the bony claw core and keratinous sheath are significantly integrated with one another, suggesting that they function as a single unit. Therefore, it is likely possible to compare fossil bony cores with extant keratinous sheaths after applying corrections. Finally, traditional metrics and geometric morphometric shape are significantly, yet loosely correlated, and geometric morphometric data better distinguish ecological groups in morphospace than is possible with traditional metrics. Based on these results, future workers are encouraged to use geometric morphometric approaches to study claw geometry and account for confounding factors such as body size, phylogeny, and individual variation prior to predicting ecology in fossil taxa.

evolutionary biology↗

bioRxiv2019

Community-level signatures of ecological succession in natural bacterial communities

A central goal in microbial ecology is to simplify the extraordinary biodiversity that inhabits natural environments into ecologically coherent units. We present an integrative top-down analysis of over 700 bacterial communities sampled from water-filled beech tree-holes in the United Kingdom at distances between <5m to >100km, combining an analyses of community composition (16S rRNA sequencing) with assays of community functional capacity (exo-enzymatic activities, ATP production, CO2 dissipation and yield). The communities were grown in laboratory conditions in a complex growth medium, what allowed us to investigate the relationship between composition and function, excluding confounding environmental factors. We found a distance-decay trend in the similarity of the communities, and simulated data allowed us to reject the hypothesis that stochastic processes dominated the assembly of the communities, suggesting that niche effects prevailed. Consistent with this idea, clustering of communities lead us to identify six distinct community classes encompassing samples collected at often distant locations. Using structural equation modelling, we explored how functions were interrelated, demonstrating that a representative functional signature can be associated with each community class. We obtained a more mechanistic understanding of the classes using metagenomic predictions with PiCRUST. Notably, this approach allowed us to show that these classes contain distinct genetic repertoires reflecting community-level ecological strategies. We finally formulated an over-arching ecological hypothesis about how local conditions drive succession in these habitats. The ecological strategies resemble the classical distinction between r- and K-strategists and could be extrapolated to other systems, suggesting that a coarse grained picture of microbial ecological succession may be explained by relatively simple ecological mechanisms.

microbiology↗

bioRxiv2019

The late blooming amphipods: global change promoted post-Jurassic ecological radiation despite Palaeozoic origin

The ecological radiation of amphipods is striking among crustaceans. Despite high diversity, global distribution and key roles in all aquatic environments, little is known about their ecological transitions, evolutionary timescale and phylogenetic relationships. It has been proposed that the amphipod ecological diversification began in the Late Palaeozoic. By contrast, due to their affinity for cold/oxygenated water and absence of pre-Cenozoic fossils, we hypothesized that the ecological divergence of amphipods arose throughout the cool Late Mesozoic/Cenozoic. We tested our hypothesis by inferring a large-scale, time-calibrated, multilocus phylogeny, and reconstructed evolutionary patterns for major ecological traits. Although our results reveal a Late Palaeozoic amphipod origin, diversification and ecological divergence ensued only in the Late Mesozoic, overcoming a protracted stasis in marine littoral habitats. Multiple independent post-Jurassic radiations took place in deep-sea, freshwater, terrestrial, pelagic and symbiotic environments, usually postdating deep-sea faunal extinctions, and corresponding with significant climatic cooling, tectonic reconfiguration, continental flooding, and increased oceanic oxygenation. We conclude that the profound Late Mesozoic global changes triggered a tipping point in amphipod evolution by unlocking ecological opportunities that promoted radiation into many new niches. Our study also provides a solid, time-calibrated, evolutionary framework to accelerate research on this overlooked, yet globally important taxon.

evolutionary biology↗

bioRxiv2018

Revealing biases in the sampling of ecological interaction networks

The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases in both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly heterogeneous. These issues may affect the accuracy of empirically constructed ecological networks. Yet statistical biases introduced by sampling error are difficult to quantify in the absence of full knowledge of the underlying ecological networks structure. To explore properties of large-scale modular networks, we developed EcoNetGen, which constructs and samples networks with predetermined topologies. These networks may represent a wide variety of communities that vary in size and types of ecological interactions. We sampled these networks with different sampling designs that may be employed in field observations. The observed networks generated by each sampling process were then analyzed with respect to the number of components, size of components and other network metrics. We show that the sampling effort needed to estimate underlying network properties accurately depends both on the sampling design and on the underlying network topology. In particular, networks with random or scale-free modules require more complete sampling to reveal their structure, compared to networks whose modules are nested or bipartite. Overall, the modules with nested structure were the easiest to detect, regardless of sampling design. Sampling according to species degree (number of interactions) was consistently found to be the most accurate strategy to estimate network structure. Conversely, sampling according to module (representing different interaction types or taxa) results in a rather complete view of certain modules, but fails to provide a complete picture of the underlying network. We recommend that these findings be incorporated into field sampling design of projects aiming to characterize large species interactions networks to reduce sampling biases.\n\nAuthor SummaryEcological interactions are commonly modeled as interaction networks. Analyses of such networks may be sensitive to sampling biases and detection issues in both the interactors and interactions (nodes and links). Yet, statistical biases introduced by sampling error are difficult to quantify in the absence of full knowledge of the underlying networks structure. For insight into ecological networks, we developed software EcoNetGen (available in R and Python). These allow the generation and sampling of several types of large-scale modular networks with predetermined topologies, representing a wide variety of communities and types of ecological interactions. Networks can be sampled according to designs employed in field observations. We demonstrate, through first uses of this software, that underlying network topology interacts strongly with empirical sampling design, and that constructing empirical networks by starting with highly connected species may be the give the best representation of the underlying network.

ecology↗

bioRxiv2014

mangal - making ecological network analysis simple

The study of ecological networks is severely limited by (i) the difficulty to access data, (ii) the lack of a standardized way to link meta-data with interactions, and (iii) the disparity of formats in which ecological networks themselves are represented. To overcome these limitations, we conceived a data specification for ecological networks. We implemented a database respecting this standard, and released a R package (rmangal) allowing users to programmatically access, curate, and deposit data on ecological interactions. In this article, we show how these tools, in conjunctions with other frameworks for the programmatic manipulation of open ecological data, streamlines the analysis process, and improves eplicability and reproducibility of ecological networks studies.

Ecology↗

bioRxiv2015

Sampling networks of ecological interactions

O_LISampling ecological interactions presents similar challenges, problems, potential biases, and constraints as sampling individuals and species in biodiversity inventories. Interactions are just pairwise relationships among individuals of two different species, such as those among plants and their seed dispersers in frugivory interactions or those among plants and their pollinators. Sampling interactions is a fundamental step to build robustly estimated interaction networks, yet few analyses have attempted a formal approach to their sampling protocols.\nC_LIO_LIRobust estimates of the actual number of interactions (links) within diversified ecological networks require adequate sampling effort that needs to be explicitly gauged. Yet we still lack a sampling theory explicitly focusing on ecological interactions.\nC_LIO_LIWhile the complete inventory of interactions is likely impossible, a robust characterization of its main patterns and metrics is probably realistic. We must acknowledge that a sizable fraction of the maximum number of interactions Imax among, say, A animal species and P plant species (i.e., Imax = AP) is impossible to record due to forbidden links, i.e., life-history restrictions. Thus, the number of observed interactions I in robustly sampled networks is typically I << Imax, resulting in extremely sparse interaction matrices with low connectance.\nC_LIO_LIReasons for forbidden links are multiple but mainly stem from spatial and temporal uncoupling, size mismatches, and intrinsically low probabilities of interspecific encounter for most potential interactions of partner species. Ad-equately assessing the completeness of a network of ecological interactions thus needs knowledge of the natural history details embedded, so that for-bidden links can be \"discounted\" when addressing sampling effort.\nC_LIO_LIHere I provide a review and outline a conceptual framework for interaction sampling by building an explicit analogue to individuals and species sampling, thus extending diversity-monitoring approaches to the characterization of complex networks of ecological interactions. This is crucial to assess the fast-paced and devastating effects of defaunation-driven loss of key ecological interactions and the services they provide and the analogous losses related to interaction gains due to invasive species and biotic homogenization.\nC_LI

Ecology↗