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Systematic variability enhances the reproducibility of an ecological study

Many scientific disciplines currently are experiencing a \"reproducibility crisis\" because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduces reproducibility by amplifying impacts of lab-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that the deliberate introduction of controlled systematic variability (CSV) in experimental designs can increase reproducibility. We tested this hypothesis using a multi-laboratory microcosm study in which the same ecological experiment was repeated in 14 laboratories across Europe. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility also was lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the \"reproducibility crisis\", deliberately including genetic variation may be a simple solution for increasing the reproducibility of ecological studies performed in controlled environments.

Ecology

Ecological and demographic drivers of jellyfish blooms

O_LIJellyfish blooms are conspicuous demographic events with significant ecological and socio-economic impact. Despite worldwide concern about an increased frequency and intensity of jellyfish mass occurrences, predicting their booms and busts remains challenging. C_LIO_LIForecasting how jellyfish populations may respond to environmental change requires taking into account their complex life histories. Metagenic life cycles, which include a benthic polyp stage, can boost jellyfish outbreaks via asexual recruitment of pelagic medusae. C_LIO_LIHere we present stage-structured matrix population models with demographic rates of all life stages of the cosmopolitan jellyfish Aurelia aurita s. l. for different environments. We investigate the life stage-dynamics of such complex populations to illustrate how changes in medusa density depend on non-medusa stage dynamics. C_LIO_LIWe show that increased food availability is an important ecological driver of jellyfish mass occurrence, as it can shift the population structure from polyp- to medusa-dominated. Projecting populations for a winter warming scenario additionally enhanced the booms and busts of jellyfish blooms. C_LIO_LIWe identify demographic key variables that control the intensity and frequency of jellyfish blooms in response to anthropogenic drivers such as habitat eutrophication and climate change. By contributing to an improved understanding of mass occurrence phenomena, our findings provide perspective for future management of ecosystem health. C_LI

ecology

Biological invasions in rodent communities: from ecological interactions to zoonotic bacterial infection issues

Several hypotheses (such as enemy release, novel weapon, spillback and dilution/density effect) suggest changes in host-parasite ecological interactions during biological invasion events. Such changes can impact both invasion process outcome and the dynamics of exotic and/or endemic zoonotic diseases. To evaluate these predictions, we investigated the ongoing invasions of the house mouse Mus musculus domesticus, and the black rat, Rattus rattus, in Senegal (West Africa). We focused on zoonotic bacterial communities depicted using 16S rRNA amplicon sequencing approach in both invasive and native rodents sampled along two well-defined invasion routes. Overall, this study provided new ecological evidence connecting parasitism and rodent invasion process, with diverse potential roles of zoonotic bacteria in the invasion success. Our results also highlighted the main factors that lie behind bacterial community structure in commensal rodents. Further experimental studies as well as comparative spatio-temporal surveys are necessary to decipher the actual role of zoonotic bacteria in these invasions. Our data also gave new support for the difficulty to predict the direction in which the relationship between biodiversity changes and disease risk could go. These results should be used as a basis for public health prevention services to design reservoir monitoring strategies based on multiple pathogen surveillance.

ecology

Simple rules for an efficient use of Geographic Information Systems in molecular ecology

Geographic Information Systems (GIS) are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and livestock species is becoming a trend with many researchers publishing genomic data that is specifically suitable for landscape studies. GIS uniquely reveal the possibility to overlay genetic information with environmental data and, as such, allow us to locate and analyze genetic boundaries of various plant and animal species or to study gene-environment associations (GEA). This means that, using GIS, we can potentially identify the genetic bases of species adaptation to particular geographic conditions or to climate change. However, many biologists are not familiar with the use of GIS and underlying concepts and thus experience difficulties in finding relevant information and instructions on how to use them. In this paper, we illustrate the power of free and open source GIS approaches and provide essential information for their successful application in molecular ecology. First, we introduce key concepts related to GIS than are too often overlooked in the literature, for example coordinate systems, GPS accuracy and scale. We then provide an overview of the most employed open-source GIS-related software, file formats and refer to major environmental databases. We also reconsider sampling strategies as high costs of Next Generation Sequencing (NGS) data currently diminish the number of samples that can be sequenced per location. Thereafter, we detail methods of data exploration and spatial statistics suited for the analysis of large genetic datasets. Finally, we provide suggestions to properly edit maps and to make them as comprehensive as possible, either manually or trough programming languages.

ecology

Last And Corresponding Authorship Practices In Ecology

Authorship is intended to convey information regarding credit and responsibility for manuscripts. However, while there is general agreement within ecology that the first author is the person who contributed the most to a particular project, there is less agreement regarding whether being last author is a position of significance and regarding what is indicated by someone being the corresponding author on a manuscript. Using an analysis of papers published in American Naturalist, Ecology, Evolution, and Oikos, I found that: 1) the number of authors on papers is increasing over time; 2) the proportion of first authors as corresponding author has increased over time, as has the proportion of last authors as corresponding author; 3) 84% of papers published in 2016 had the first author as corresponding author; and 4) geographic regions differed in the likelihood of having the first (or last) author as corresponding author. I also carried out an online survey to better understand views on last and corresponding authorship. This survey revealed that most ecologists view the last author as the \"senior\" author on a paper (that is, the person who runs the research group in which most of the work was carried out), and most ecologists view the corresponding author as the person taking full responsibility for a paper. However, there was substantial variation in views on authorship, especially corresponding authorship. Given these results, I suggest that discussions of authorship have as their starting point that the first author will be corresponding author and the senior author will be last author. I also suggest ways of deciding author order in cases where two senior authors contributed equally.

ecology

Generic assembly patterns in large ecological communities

The study of ecological communities often involves detailed simulations of complex networks. But our empirical knowledge of these networks is typically incomplete, and the space of simulation models and parameters is vast, leaving room for uncertainty in theoretical predictions. Here, we show that a large fraction of this space of possibilities exhibits generic behaviors that are robust to modelling choices. We consider a wide array of model features, including interaction types and community structures, known to generate different dynamics for a few species. We combine these features in large simulated communities, and show that equilibrium diversity, functioning and stability can be predicted analytically using a random model parameterized by a few statistical properties of the community. We give an ecological interpretation of this \"disordered\" limit where structure fails to emerge from complexity. We also demonstrate that some well-studied interaction patterns remain relevant in large ecosystems, but their impact can be encapsulated in a minimal number of additional parameters. Our approach provides a powerful framework for predicting the outcomes of ecosystem assembly and quantifying the added value of more detailed models and measurements.

ecology

The prevalence and impact of transient species in ecological communities

Transient species occur infrequently in a community over time and do not maintain viable local populations. Because transient species interact differently than non-transients with their biotic and abiotic environment, it is important to characterize the prevalence of these species and how they impact our understanding of ecological systems. We quantified the prevalence and impact of transient species in communities using data on over 17,000 community time series spanning an array of ecosystems, taxonomic groups, and spatial scales. We found that transient species are a general feature of communities regardless of taxa or ecosystem. The proportion of these species decreases with spatial scale leading to a need to control for scale in comparative work. Removing transient species from analyses influences the form of a suite of commonly studied ecological patterns including species-abundance distributions, species-energy relationships, species-area relationships, and temporal turnover. Careful consideration should be given to whether transient species are included in analyses depending on the theoretical and practical relevance of these species for the question being studied.

ecology

A mechanistic perspective of ecological networks highlights the contribution of alternative interaction strategies

O_LISpecies traits mediate ecological interaction outcomes and community structure. It is important, therefore, to identify the minimum number of traits required to characterise observed networks, i.e. the minimum dimensionality. Existing methods for estimating minimum dimensionality often lack three features commonly associated with a higher numbers of traits: a mechanistic description of observed interactions, alternative interaction modes (e.g. different feeding strategies such as active vs sit-and-wait feeding), and trait-mediated forbidden links. Omitting these features can lead to underestimation of the trait numbers involved, and therefore, minimum dimensionality. Here, we develop a minimum mechanistic dimensionality measure, accounting for these three features. C_LIO_LIThe only input required by our method is the observed network of interaction outcomes. We then assume how traits are mechanistically involved in alternative interaction modes. These unidentified traits are contrasted using pairwise performance inequalities between the interacting species. E.g. if a predator feeds upon a prey species via a typical predation mode, in each step of the predation sequence the predators performance must be greater than the preys. We construct a system of inequalities from all observed outcomes, which we attempt to solve with mixed integer linear programming. The minimum number of traits required for a feasible system of inequalities provides our dimensionality estimate. C_LIO_LIWe applied our method to 658 published empirical ecological networks including animal dominance, predator-prey, primary consumption, pollination, parasitism and seed dispersal networks, to compare with minimum dimensionality estimates when the three focal features are missing. Minimum dimensionality was typically higher when including alternative interaction modes (54% of empirical networks), forbidden interactions as trait-mediated interaction outcomes (92%), or a mechanistic perspective (81%), compared to network dimensionality estimates missing these features. C_LIO_LIOur method can reduce the risk of omitting essential traits that are involved mechanistically, in different interaction modes, or in failure outcomes. More accurate estimates will allow us to parameterise models to generate theoretical networks with a more realistic structure at the interaction outcome level. Thus, we hope our method can improve predictions of community structure and structure-dependent dynamics. C_LI

ecology

FENNEC - Functional Exploration of Natural Networks and Ecological Communities

O_LISpecies composition assessment of ecological communities and networks is an important aspect of biodiversity research. Yet often ecological traits of organisms in a community are more informative than scientific names only. Furthermore, other properties like threat status, invasiveness, or human usage are relevant for many studies, but cannot be evaluated from taxonomy alone. Despite public databases collecting such information, it is still a tedious manual task to enrich community analyses with such, especially for large-scaled data.\nC_LIO_LIThus we aimed to develop a public and free tool that eases bulk trait mapping of community data in a web browser, implemented with current standard web and database technologies.\nC_LIO_LIHere we present the FO_SCPLOWENNECC_SCPLOW, a workbench that eases the process of mapping publicly available trait data to the users communities in an automated process. Usage is either by a local self-hosted or a public instance (https://fennec.molecular.eco) covering exemplary traits. Alongside the software we also provide usage and hosting documentation as well as online tutorials.\nC_LIO_LIThe FO_SCPLOWENNECC_SCPLOW aims to motivate public trait data submission and its reuse in meta-analyses. Further, it is an open-source development project with the code freely available to use and open for community contributions (https://github.com/molbiodiv/fennec).\nC_LI

ecology

Interconnections accelerate collapse in a socio-ecological metapopulation

Resource over-exploitation can have profound effects on both ecosystems and the human populations residing in them. Models of population growth based on a depletable resources have been studied previously, but relatively few consider metapopulation effects. Here we analyze a socio-ecological metapopulation model where resources grow logistically on each patch. Each population harvests resources on its own patch to support population growth, but can also harvest resources from other patches when their own patch resources become scarce. We find that allowing populations to harvest from other patches significantly accelerates collapse and also increases the parameter regime for which collapse occurs, compared to a model where populations are not able to harvest resources from other patches. As the number of patches in the metapopulation increases, collapse is more sudden, more severe, and occurs sooner. These effects also persist under scenarios of asymmetry and inequality between patches. We conclude that metapopulation effects in socio-ecological systems can be both helpful and harmful and therefore require urgent study.

ecology

Rethinking the importance of ecological networks through the glass of environmental variations

A major quest in network and community ecology has been centered on understanding the importance of structural patterns in species interaction networks--the synthesis of who interacts with whom in a given location and time. In the past decades, much effort has been devoted to infer the importance of a particular structure by its capacity to tolerate an external perturbation on its structure or dynamics. Here we demonstrate that such a perspective leads to inconsistent conclusions. That is, the importance of a network structure changes as a function of the external perturbations acting on a community at any given point in time. Thus, we discuss a research agenda to investigate the relative importance of the structure of ecological networks under an environment-dependent framework. We hypothesize that only by studying systematically the link between network structure and community dynamics under an environment-dependent framework, we can uncover the limits at which communities can tolerate environmental changes.\n\n\"Variation stands out as the only meaningful reality\"\n\nStephen J. Gould.

ecology

Gender-biased perceptions of important ecology articles

Gender bias is still unfortunately rife in the sciences, and men co-author most articles (> 70%) in ecology. Whether ecologists subconsciously rate the quality of their peers work more favourably if men are the dominant co-authors is still unclear. To test this hypothesis, we examined how expert ecologists ranked important ecology articles based on a previously compiled list. Women proposed articles with a higher average proportion of women co-authors (0.18) than did men proposers (0.07). For the 100 top-ranked articles, women voters placed more emphasis on articles co-authored by women (0.06) than did men (0.02). However, women voters were still biased because they ranked men-dominated articles more highly, albeit not by as much as men did. This effect disappeared after testing read-only articles. This indicates a persistent, subconscious bias that men-dominated articles are considered to be of higher quality before actual assessment. We add that ecologists need to examine their own subconscious biases when appointing students, hiring staff, and choosing colleagues with whom to publish.

ecology

Identifying Important Interaction Modifications in Ecological Systems

Trophic interaction modifications, where a consumer-resource link is affected by additional species, are widespread and significant causes of indirect effects in ecological networks. The sheer number of potential interaction modifications in ecological systems poses a considerable challenge, making prioritisation for empirical study essential. Here, we introduce measures to quantify the topological relationship of individual interaction modifications relative to the underlying network. We use these, together with measures for the strength of trophic interaction modifications to identify modifications that are most likely to exert significant effects on the dynamics of whole systems. Using a set of simulated food webs and randomly distributed interaction modifications, we test whether a subset of interaction modifications important for the local stability and direction of species responses to perturbation of complex networks can be identified. We show that trophic interaction modifications affecting interactions with a high biomass flux, those that connect species otherwise distantly linked, and those where high trophic-level species modify to interactions lower in the web have particular importance for dynamics. In contrast, the centrality of modifications in the network provided little information. This work demonstrates that analyses of interaction modifications can be tractable at the network scale and highlights the importance of understanding the relationship between the distributions of trophic and non-trophic effects.

ecology

Planned missing data design: stronger inferences, increased research efficiency and improved animal welfare in ecology and evolution

O_LIEcological and evolutionary research questions are increasingly requiring the integration of research fields along with larger datasets to address fundamental local and global scale problems. Unfortunately, these agendas are often in conflict with limited funding and a need to balance animal welfare concerns.\nC_LIO_LIPlanned missing data design (PMDD), where data are randomly and deliberately missed during data collection, is a simple and effective strategy to working under greater research constraints while ensuring experiments have sufficient power to address fundamental research questions. Here, we review how PMDD can be incorporated into existing experimental designs by discussing alternative design approaches and evaluating how data imputation procedures work under PMDD situations.\nC_LIO_LIUsing realistic examples and simulations of multilevel data we show how a variety of research questions and data types, common in ecology and evolution, can be aided by using a PMDD with data imputation procedures. More specifically, we show how PMDD can improve statistical power in detecting effects of interest even with high levels (50%) of missing data and moderate sample sizes. We also provide examples of how PMDD can facilitate improved animal welfare and potentially alleviate research costs and constraints that would make endeavours for integrative research challenging.\nC_LIO_LIPlanned missing data designs are still in their infancy and we discuss some of the difficulties in their implementation and provide tentative solutions. Nonetheless, data imputation procedures are becoming more sophisticated and more easily implemented and it is likely that PMDD will be an effective and powerful tool for a wide range of experimental designs, data types and problems in ecology and evolution.\nC_LI

ecology

Ecological assessment of the River Nile around Gizert El-Warrak by Phytoplankton and macroinvertebrates assemblages

Biological assessment is considered a useful tool for assessing the ecological status of the aquatic ecosystems. Therefore, the goal of the present study was to use phytoplankton and macroinvertebrates as biological tools for ecological assessment of the River Nile around Gizert El-Warrak. A total of 33 phytoplankton species identified in the studied stations; these include 16 species of Chlorophyta, 5 species of Cyanophyta and 12 species of Bacillariophyta. All investigated stations characterized by high organic pollution according to Palmer's index. Trophic state index showed a hyper-eutrophic status in stations S1, S2, S4, S6 and S8 and an eutrophic status in stations S3, S5 and S7.Gastropoda and Oligochaeta were the most dominant of macroinvertebrates taxa recorded 50.8 and 24.6%, respectively. Diversity Index (H') ranged (1.14 - 2) which indicated that the structure of macroinvertebrates habitat was poor. Also, Evenness Index (J) ranged (0.016 - 0.043) which indicated that individuals were not distributed equally. The values of biotic index depending on macroinvertebrates categories showed that the River Niles water quality is fairly poor with significant organic pollution.\n\nSummary statementBioassessment based on non-taxonomic measurements of algae and biotic indices of macroinvertebrates may be considered as vital methods that reflect disturbances in aquatic systems for both short-term and long-term.

ecology

Whence Lotka-Volterra? Conservation Laws and Integrable Systems in Ecology.

Competition in ecology is often modeled in terms of direct, negative effects of one individual on another. An example is logistic growth, modeling the effects of intraspecific competition, while the Lotka-Volterra equations for competition extend this to systems of multiple species, with varying strengths of intra- and inter-specific competition. These equations are a classic and well-used staple of quantitative ecology, providing a framework to understand species interactions, species coexistence, and community assembly. They can be derived from an assumption of random mixing of organisms, and an outcome of each interaction that removes one or more individuals. However, this framing is some-what unsatisfactory, and ecologists may prefer to think of phenomenological equations for competition as deriving from competition for a set of resources required for growth, which in turn may undergo their own complex dynamics. While it is intuitive that these frameworks are connected, and the connection is well-understood near to equilibria, here we ask the question: when can consumer dynamics alone become an exact description of a full system of consumers and resources? We identify that consumer-resource systems with this property must have some kind of redundancy in the original description, or equivalently there is one or more conservation laws for quantities that do not change with time. Such systems are known in mathematics as integrable systems. We suggest that integrability in consumer-resource dynamics can only arise in cases where each species in an assemblage requires a distinct and unique combination of resources, and even in these cases it is not clear that the resulting dynamics will lead to Lotka-Volterra competition.\n\nI acknowledge the Simons Foundation Grant #376199 and the McDonnell Foundation Grant #220020439.

ecology

Mapping Social Ecological Systems Archetypes

While sustainable development goals are by their nature global, their achievement requires local action and thus targeting and monitoring sustainable solutions tailored to different social and ecological contexts. Ostrom stressed that there are no panaceas or universal solutions to environmental problems, and developed a social-ecological systems (SES) framework -a nested multi-tier set of variables- to help diagnose problems, identify complex interactions, and solutions tailored to each SES arena. The framework has been applied to over a hundred cases, typically reflecting in-depth analysis of local case studies, but with relatively small coverage in space and time. While case studies are context rich and necessary, it can be difficult to upscale their lessons to policy making realms. Here we develop a data driven method for upscaling Ostroms SES framework and apply it to a context where data is scarce, incomplete, but also where sustainable solutions are needed. The purpose of upscaling the framework is to create a tool that facilitates decision-making on data scarce contexts such as developing countries. We mapped SES by applying the SES framework to poverty alleviation and food security issues in the Volta River basin in Ghana and Burkina Faso. We found archetypical configurations of SES in space. Given data availability, we study their change over time, and discuss where agricultural innovations such as water reservoirs might have a stronger impact at increasing food security and therefore alleviating poverty and hunger. We conclude by outlining how the method can be used in other SES comparative studies.

ecology

Ecological Network assembly: how the regional meta web influence local food webs

O_LILocal food webs result from a sequence of colonisations and extinctions by species from the regional pool or metaweb, i.e., the assembly process. Assembly is theorised to be a selective process: whether or not certain species or network structures can persist is partly determined by local processes including habitat filtering and dynamical constraints. Consequently, local food web structure should reflect these processes. C_LIO_LIThe goal of this study was to test evidence for these selective processes by comparing the structural properties of real food webs to the expected distribution given the metaweb. We were particularly interested in ecological dynamics; if the network properties commonly associated with dynamical stability are indeed the result of stability constraints, then they should deviate from expectation in the direction predicted by theory. C_LIO_LITo create a null expectation, we used the novel approach of randomly assembling model webs by drawing species and interactions from the empirical metaweb. The assembly model permitted colonisation and extinction, and required a consumer species to have at least one prey, but had no habitat type nor population dynamical constraints. Three data sets were used: (1) the marine Antarctic metaweb, with 2 local food-webs; (2) the 50 lakes of the Adirondacks; and (3) the arthropod community from Florida Keys classic defaunation experiment. C_LIO_LIContrary to our expectations, we found that there were almost no differences between empirical webs and those resulting from the null assembly model. Few empirical food webs showed significant differences with network properties, motif representations and topological roles. Network properties associated with stability did not deviate from expectation in the direction predicted by theory. C_LIO_LIOur results suggest that -- for the commonly used metrics we considered -- local food web structure is not strongly influenced by dynamical nor habitat restrictions. Instead, the structure is inherited from the metaweb. This suggests that the network properties typically attributed as causes or consequences of ecological stability are instead a by-product of the assembly process (i.e., spandrels), and may potentially be too coarse to detect the true signal of dynamical constraint. C_LI

ecology