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At least 415 records · Page 23Linked to original sources
bioRxiv2017

Estimating sampling completeness of interactions in quantitative bipartite ecological networks: incorporating variation in species specialisation

BackgroundThe analysis of ecological networks can be affected by sampling effort, potentially leading to bias. Ecological network structure is often summarised by descriptive metrics but these metrics can vary according to the proportion of the total interactions that have been observed. Therefore, to know the likely degree of bias, it is valuable to estimate the total number of interactions in a network, and so calculate the proportion of interactions that have been observed (sampling completeness of interactions). Existing approaches to estimate sampling completeness of interactions use the Chao family of asymptotic species richness estimators to predict the total number of interactions, but do not fully utilise information about the relative specialisation of species within the network.\n\nResultsHere, we propose a modification of previously-used methods, that places equal weight on each interaction (whether or not it has been observed), rather than on each species. Our approach is therefore equivalent to weighting the interaction sampling completeness of each species in the network according to its relative specialisation. We demonstrate that, for the subset of species that are observed and when assuming that species richness estimators accurately project the number of unobserved interactions per observed species, our approach is mathematically more accurate. Our approach can be universally applied to any quantitative, bipartite network.\n\nWe propose two methods to estimation using our approach, using abundance-based and incidence-based species richness estimators respectively, and give recommendations when each should be applied. We discuss the effect of unobserved species and the potential use of a threshold of minimum abundance for species inclusion. Finally, we consider these advances in the context of some of the main issues surrounding estimation of interaction sampling completeness in network ecology.\n\nConclusionsWe recommend that future studies of bipartite networks utilise our approach and methods to estimate the sampling completeness of interactions, to assist with the quantitative and comparative analysis and interpretation of network properties.

ecology↗
bioRxiv2019

Ecological drivers of African swine fever virus persistence in wild boar populations: insight for control

Environmental sources of infection can play a primary role in shaping epidemiological dynamics, however the relative impact of environmental transmission on host-pathogen systems is rarely estimated. We developed and fit a spatially-explicit model of African swine fever virus (ASFV) in wild boar to estimate what proportion of carcass-based transmission is contributing to the low-level persistence of ASFV in Eastern European wild boar. Our model was developed based on ecological insight and data from field studies of ASFV and wild boar in Eastern Poland. We predicted that carcass-based transmission would play a substantial role in persistence, especially in low-density host populations where contact rates are low. By fitting the model to outbreak data using Approximate Bayesian Computation, we inferred that between 53 to 66% of transmission events were carcass-based - i.e., transmitted through contact of a live host with a contaminated carcass. Model fitting and sensitivity analyses showed that the frequency of carcass-based transmission increased with decreasing host density, suggesting that management policies should emphasize the removal of carcasses and consider how reductions in host densities may drive carcass-based transmission. Sensitivity analyses also demonstrated that carcass-based transmission is necessary for the autonomous persistence of ASFV under realistic parameters. Autonomous persistence through direct transmission alone required high host densities; otherwise re-introduction of virus periodically was required for persistence when direct transmission probabilities were moderately high. We quantify the relative role of different persistence mechanisms for a low-prevalence disease using readily collected ecological data and viral surveillance data. Understanding how the frequency of different transmission mechanisms vary across host densities can help identify optimal management strategies across changing ecological conditions.

ecology↗
bioRxiv2020

Lineage Functional Types (LFTs): Characterizing functional diversity to enhance the representation of ecological behavior in Earth System Models

Process-based vegetation models attempt to represent the wide range of trait variation in biomes by grouping ecologically similar species into plant functional types (PFTs). This approach has been successful in representing many aspects of plant physiology and biophysics, but struggles to capture biogeographic history and ecological dynamics that determine biome boundaries and plant distributions. Grass dominated ecosystems are broadly distributed across all vegetated continents and harbor large functional diversity, yet most Earth System Models (ESMs) summarize grasses into two generic PFTs based primarily on differences between temperate C3 grasses and (sub)tropical C4 grasses. Incorporation of species-level trait variation is an active area of research to enhance the ecological realism of PFTs, which form the basis for vegetation processes and dynamics in ESMs. Using reported measurements, we developed grass functional trait values (physiological, structural, biochemical, anatomical, phenological, and disturbance-related) of dominant lineages to improve ESM representations. Our method is fundamentally different from previous efforts, as it uses phylogenetic relatedness to create lineage-based functional types (LFTs), situated between species-level trait data and PFT-level abstractions, thus providing a realistic representation of functional diversity and opening the door to the development of new vegetation models.

ecology↗
bioRxiv2020

Ecological Relationships in the Serengeti National Park

The use of camera traps in animal ecology has transformed the field by allowing a greater quantity of detailed observations with limited human interference. One of largest camera trap studies published to date is from the Serengeti National Park (SNP) in Tanzania, East Africa which deployed 225 camera traps and obtained over 1.2 million pictures. This paper will focus primarily on the top predator of the Serengeti, the lion, and how it affects and is affected by prey, subordinate predators and the dramatic shift in the seasons. I asked the following three questions to better understand species relationships in the SNP: 1) Do the seasons in the SNP have an effect on the RAB of lions? 2) Does the presence or absence of lions have an effect on the RAB of hyenas in the wet season? 3) Does the presence/absence of Thompson gazelles (Eudorcas thomsonii) and impalas (Aepyceros melampus) in the wet season have an effect on the RAB of lions? During the dry and wet season of 2012 in the SNP there did not appear to be a change in the relative abundance of lions (Fig. 1), nor did lion relative abundance affect hyenas. The lions might possibly alter their diet during the dry seasons to include non-migratory species and choose not to change their territory on a season to season basis. Based on these findings research should focus on how the lions adapt to the changes in prey abundance during the wet and dry season. This preliminary analysis of the ecological dynamics of lions and associated species in the SNP is intriguing and yet raises significantly more questions than it has answered. Additional research surrounding the effects of yearly migration on the lions home territory, diet, and species interactions should be investigated more thoroughly, to greater understand the ecological relationships in the SNP. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/895409v1_fig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@1808f9corg.highwire.dtl.DTLVardef@15453beorg.highwire.dtl.DTLVardef@145e6ceorg.highwire.dtl.DTLVardef@341460_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO The relative abundance of lions in the dry and wet season in the Serengeti National Park observed by162 camera traps during 2012. Lion relative abundance (RAB) is given in units of the number of events in 100 trap nights. RAB values were determined by using motion censored cameras to identify the presence of a Lion and then disregarding all sightings for a 30-minute period following initial observation. This sighting/identification was referred to as an event. The total number of events for each camera was calculated and divided by the number of trap nights the camera was operational. The value was then multiplied by 100 to give the number of events per 100 trap nights. P-value > 0.05. C_FIG

ecology↗
bioRxiv2020

Ecological success of sexual and asexual reproductive strategies invading an environmentally unstable habitat

Many aspects of sexual and asexual reproduction have been studied empirically and theoretically. The differences between sexual and asexual reproduction within a species often lead to a biased geographical distribution of individuals with different reproductive strategies. While sexuals are more abundant in the core habitat, asexuals are often found in marginal habitats along the edge of the species distribution. This pattern, called geographic parthenogenesis, has been observed in many species but the mechanisms reponsible for generating it are poorly known. We used a quantitative approach using a metapopulation model to explore the ecological processes that can lead to geographic parthenogenesis and the invasion of new habitats by different reproductive strategies. We analyzed the Allee effect on sexual populations and the population sensitivity to environmental stress during the invasion of a marginal, unstable habitat to demonstrate that a complex interaction between the Allee effect, sensitivity to environmental stress and the environmental conditions can determine the relative success of competing reproductive strategies during the initial invasion and longterm establishment in the marginal habitat. We discuss our results in the light of previous empirical and theoretical studies. Author SummaryIndividuals can reproduce with or without sex. Very often, closely related species are distributed in a such a way that the sexually reproducing species is most frequently found in the core habitat while the asexually reproducing species is found on the edge of the habitat range. This biased distribution of reproductive strategies across a habitat range is called geographic parthenogenesis and has been observed in several species. While many processes have been proposed to explain such a pattern, a quantitative approach of the ecological processes was absent. We investigated important differences between sexual and asexual reproduction and how these differences affect the success of sexuals and asexuals invading a marginal, unstable environment. We showed that the relative frequency of each reproductive strategy in the marginal habitat depends on how much sexuals rely on population density to reproduce and how much asexuals are affected by environmental stress relative to sexuals. Our study presents a quantitative ecological explanation for geographic parthenogenesis and provides the conditions under which different distribution patterns can emerge.

ecology↗
bioRxiv2020

Generation and application of river network analogues for use in ecology and evolution

O_LISeveral key processes in freshwater ecology and evolution are governed by the connectivity inherent to dendritic river networks. These networks have extensively been analyzed from a geomorphological and hydrological viewpoint, yet network structures classically used in modelling have only been partially representative of the structure of real river basins, and have often failed to capture well known scaling features of real river networks. Pioneering work has identified optimal channel networks (OCNs) as spanning trees that reproduce all scaling features characteristic of real, natural stream networks worldwide. While these networks have been used to generate landscapes for studies on metapopulations, biodiversity and epidemiology, their generation has not been generally accessible. C_LIO_LIGiven the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we also provide the R-package OCNet. Owing to the random search process that generates OCNs, multiple network replicas spanning the same surface can be built, allowing one to perform computational experiments whose results do not depend on the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three-dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the OCNet package provides functions that aggregate the OCN into an arbitrary number of nodes, calculate several metrics and descriptors of river networks, and draw relevant features of the network. C_LIO_LIWe describe the main functionalities of the package and present how it can be integrated into other R-packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species. C_LIO_LIIn conclusion, OCNet provides a powerful tool to generate and use realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems, and enhances our knowledge on spatial processes in freshwater ecology in general. C_LI

ecology↗
bioRxiv2020

Repeatable ecological dynamics govern response of experimental community to antibiotic pulse perturbation

In an era of pervasive anthropogenic ecological disturbances, there is a pressing need to understand the factors constituting community response and resilience. A detailed understanding of disturbance response needs to go beyond associations and incorporate features of disturbances, species traits, rapid evolution and dispersal. Multispecies microbial communities experiencing antibiotic perturbation represent a key system with important medical dimensions. However, previous microbiome studies on the theme have relied on high-throughput sequencing data from uncultured species without the ability to explicitly account for the role of species traits and immigration. Here we serially passaged a 34-species defined bacterial community through different levels of pulse antibiotic disturbance, manipulating the presence or absence of species immigration. To understand the ecological community response measured by amplicon sequencing, we combined initial trait data measured for each species separately and metagenome sequencing data revealing adaptive mutations during the experiment. We found that the ecological community response was highly repeatable within the experimental treatments, owing to an increasingly strong yet canalized response at increasing antibiotic levels, which could be partly attributed to key species traits (antibiotic susceptibility and growth rate). Increasing antibiotic levels were also coupled with increasing species extinction probability, making species immigration preventing this critical for community resilience. Moreover, we could detect signals of antibiotic resistance evolution occurring within species at the same time scale, leaving evolutionary changes in communities despite recovery at the species compositional level. Together these observations reveal a disturbance response which appears as classic species sorting but is nevertheless accompanied by rapid within-species evolution.

ecology↗
bioRxiv2020

Lipids as currency in ecological interactions: Competition and facilitation between two lipid scavenging parasitoids

Interspecific interactions in nature often revolve around the acquisition of nutrients. Depending on the organisms metabolic requirements, competition for specific essential nutrients may occur, which selects for increased abilities to monopolize, consume and store these nutrients. Lipid scavengers are organisms that rely on exogenous lipid acquisition as they lack the ability to synthesize fatty acids de novo or in sufficient quantity. Most parasitoid insects are lipid scavengers: they obtain all required lipids by feeding on their hosts as larvae. Here we study the nutritional ecology of competitive interactions between native Nasonia vitripennis and introduced Tachinaephagus zealandicus. While the former was already known to lack lipogenesis, we show that T. zealandicus also relies on host lipids. The interactions between the two species were studied using competition experiments, in which oviposition of T. zealandicus on a host was followed by multiparasitism by N. vitripennis. The outcome of competition was determined by the duration of the time lag between oviposition events. N. vitripennis was superior when arriving 3 days after oviposition by T. zealandicus. In contrast, 9 days after oviposition of T. zealandicus we observed complete reversal, and no N. vitripennis offspring were able to develop. Only when N. vitripennis laid eggs 15 days after T. zealandicus oviposition, both species could emerge from the same host. However, N. vitripennis realizes only 10% of its potential fitness at this time point because prior parasitization by the gregarious T. zealandicus compartmentalizes the host resources, limiting the spread of N. vitripennis venom. This study shows that successful reproduction of N. vitripennis at 15 days was achieved by hyperparasitizing, a capability that provides a fitness benefit to N. vitripennis, as it extends the time window that hosts are available for parasitization. Choice tests with hosts at different time intervals after T. zealandicus oviposition revealed a partial mismatch in N. vitripennis females between competition avoidance and offspring performance, which may be linked to the limited co-evolutionary time between native and introduced species. We discuss our results in the context of nutritional ecology and, specifically, the role of lipids in ecological interactions.

ecology↗
bioRxiv2020

SSP: An R package to estimate sampling effort in studies of ecological communities

SSP (simulation-based sampling protocol) is an R package that uses simulation of ecological data and dissimilarity-based multivariate standard error (MultSE) as an estimator of precision to evaluate the adequacy of different sampling efforts for studies that will test hypothesis using permutational multivariate analysis of variance. The procedure consists in simulating several extensive data matrixes that mimic some of the relevant ecological features of the community of interest using a pilot data set. For each simulated data, several sampling efforts are repeatedly executed and MultSE calculated. The mean value, 0.025 and 0.975 quantiles of MultSE for each sampling effort across all simulated data are then estimated and standardized regarding the lowest sampling effort. The optimal sampling effort is identified as that in which the increase in sampling effort do not improve the precision beyond a threshold value (e.g. 2.5 %). The performance of SSP was validated using real data, and in all examples the simulated data mimicked well the real data, allowing to evaluate the relationship MultSE - n beyond the sampling size of the pilot studies. SSP can be used to estimate sample size in a wide range of situations, ranging from simple (e.g. single site) to more complex (e.g. several sites for different habitats) experimental designs. The latter constitutes an important advantage, since it offers new possibilities for complex sampling designs, as it has been advised for multi-scale studies in ecology.

ecology↗
bioRxiv2020

Ecologically relevant thermal fluctuations enhance offspring fitness: biological and methodological implications for studies of thermal developmental plasticity

Natural thermal environments are notably complex and challenging to mimic in controlled studies. Consequently, our understanding of the ecological relevance and underlying mechanisms of organismal responses to thermal environments is often limited. For example, studies of thermal developmental plasticity have provided key insights into the ecological consequences of temperature variation, but most laboratory studies use treatments that do not reflect natural thermal regimes. While controlling other important factors, we compared the effects of naturally fluctuating temperatures to commonly used laboratory regimes on development of lizard embryos and offspring phenotypes and survival. We incubated eggs in 4 treatments - 3 that followed procedures commonly used in the literature, and one that precisely mimicked naturally fluctuating nest temperatures. To explore context-dependent effects, we replicated these treatments across two seasonal regimes: relatively cool temperatures from nests constructed early in the season and warm temperatures from late-season nests. We show that natural thermal fluctuations have a relatively small effect on developmental variables but enhance hatchling performance and survival at cooler temperatures. Thus, natural thermal fluctuations are important for successful development and simpler approximations (e.g. repeated sine waves, constant temperatures) may poorly reflect natural systems under some conditions. Thus, the benefits of precisely replicating real-world temperatures in controlled studies may outweigh logistical costs. Although patterns might vary according to study system and research goals, our methodological approach demonstrates the importance of incorporating natural variation into controlled studies and provides biologists interested in thermal ecology with a framework for validating the effectiveness of commonly used methods.

ecology↗
bioRxiv2020

Extreme ecological specialization in a rainforest mammal, the Bornean tufted ground squirrel, Rheithrosciurus macrotis

The endemic Bornean tufted ground squirrel, Rheithrosciurus macrotis, has attracted great interest among biologists and the public recently. Nevertheless, we lack information on the most basic aspects of its biology. Here we present the first empirical data on the feeding ecology of tufted ground squirrels, and use data from 81 sympatric mammalian and avian vertebrates to place it within a broad comparative context. R. macrotis is a dedicated seed predator and shows much more extreme ecological specialization than any other vertebrate, feeding on a far smaller subset of available plant foods and demonstrating a greater reliance on a single plant species- Canarium decumanum-than any other vertebrate taxon. Our results suggest that R. macrotis plays an important, previously unknown role in the ecology of Bornean lowland forests, and highlight how much we have yet to learn about the fauna inhabiting some of the most diverse, and most severely threatened, ecosystems on the planet.

ecology↗
bioRxiv2020

Evaluation method of ecosystem service value under complex ecological environment: A case study of Gansu Province, China

Scientific assessment of regional ecosystem service value (ESV) is helpful to make scientific ecological protection plan and compensation policy. The evaluation method has not been established that is adapted to the complex and diverse characteristics of the ecological environment. This paper takes Gansu Province as an example, on the basis of fully considering the regional differences of ecosystem service function, the five correction index of value equivalent factor per unit area were constructed in the provincial scale, and the regional difference adjustment index of 11 kinds of ES was constructed in regional scale, in the way, the value evaluation model based on regional difference was established. The results show that in 2015, the total ESV reached 2239.555 billion Yuan in Gansu Province, ESV gradually increased from the northeast to the southwest, and the high-value areas of service function located in Qilian Mountain and Longnan Mountain, of which the forest and grassland ecosystem contributed the most to the value. From the perspective of value composition, local climate regulation and biodiversity maintenance function are the main service functions of Gansu Province. From 2000 to 2015, ESV increased by 3.426 billion Yuan in Gansu Province, the value of forest and urban ecosystem continued increasing, while the value of cultivated land ecosystem continue decreasing. From the spatial characteristics of service value change, the area of value reduction gradually moved from the central part of Gansu Province to the surrounding area. In general, although this study needs further improvement, the constructed evaluation method provides a relatively comprehensive evaluation scheme for the spatiotemporal dynamic evaluation of ESV in Gansu Province. This study provided a more overall research idea for the evaluation of ESV under complex ecological environment.

ecology↗
bioRxiv2020

Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae

Harmful algae can have profound economic, environmental, and social consequences. As the timing, frequency, and severity of harmful algal blooms (HABs) change alongside global climate, efficient tools to monitor and understand the current ecological context of these taxa are increasingly important. Here we employ environmental DNA metabarcoding to identify patterns in a wide variety of harmful algae and associated ecological communities in the Hood Canal of Puget Sound in Washington State, USA. We track trends of presence and abundance in a series of water samples across nearly two years. We find putative harmful algal sequences in a majority of samples, suggesting that these groups are routinely present in local waters. We report patterns in variants of the economically important genus Pseudo-nitzschia (family Bacillariaceae), as well as multiple harmful algal taxa previously unknown or poorly documented in the region, including a cold-water variant from the saxitoxin-producing genus Alexandrium (family Gonyaulacaceae), two variants from the karlotoxin-producing genus Karlodinium (family Kareniaceae), and one variant from the parasitic genus Hematodinium (family Syndiniaceae). We then use data on environmental variables and the biological community surrounding each algal taxon to illustrate the ecological context in which these species are commonly found. Environmental DNA metabarcoding thus simultaneously (1) alerts us to potential new or cryptic occurrences of harmful algae, (2) expands our knowledge of the co-occurring conditions and species associated with the growth of these organisms in changing marine environments, and (3) provides a tool for monitoring and management moving forward.

ecology↗
bioRxiv2020

Biogeographical and ecological factors associated with kill rates of an apex predator

AO_SCPLOWBSTRACTC_SCPLOWKill rates and functional responses are fundamental to the study of predator ecology and the understanding of predatory-prey dynamics. As the most widely distributed apex predator in the western hemisphere pumas (Puma concolor) have been widely studied yet a biogeographical synthesis of their kill rates is currently lacking. We reviewed the literature and compiled data on sex- and age-specific kill rate estimates of pumas on ungulates, and conducted analyses aimed at understanding ecological factors explaining the observed variation across their range. Kill rate studies on pumas, while numerous, were primarily conducted in Temperate Conifer Forests (< 10% of puma range), revealing a dearth of knowledge across much of their range, especially from tropical and subtropical habitats. Across studies, kill rates in ungulates/week were highest for adult females with kitten(s) (1.24 {+/-} 0.41 ungulates/week) but did not vary significantly between adult males (0.84 {+/-} 0.18) and solitary adult females (0.99 {+/-} 0.26). Kill rates in kg/day did not differ significantly among reproductive classes. Kill rates of adult pumas increased with ungulate density. Ungulate species richness had a weak negative association with adult male kill rates. Neither scavenger richness, the proportion of non-ungulate prey in the diet, nor regional human population density had a significant effect on ungulate kill rates. Our results had a strong temperate-ecosystem bias highlighting the need for further research across the diverse biomes pumas occupy in order to make species level inferences. Data from more populations would also allow for multivariate analyses providing deeper inference into the ecological and behavioural factors driving kill rates and functional responses of pumas, and apex predators in general.

ecology↗
bioRxiv2020

In-stream habitat availability for river dolphins in response to flow: use of ecological integrity to manage river flows

Population decline and extinction risk of riverine cetaceans are primarily associated with flow alteration. Previous studies predominantly highlighted maintenance of adequate flow for low water seasons when habitats contract and the risk of local extinction escalates. Although riverine cetaceans are sensitive to reduction in river flow, no studies quantify the relationships between flow and ecology of riverine cetaceans to mitigate the potential adverse impacts of flow alteration. We quantify the relationships between flow and the ecology of river cetaceans with reference to Ganges River dolphins (GRD; Platanista gangetica gangetica) usable area availability (AWS) for the low water season at wider flows (50-575 m3/s) at finer spatial and temporal scales. This study reveals that distribution of usable area to GRD highly regulated by the adequate flow level as the interaction of appropriate velocity and depth at particular geomorphic that likely offer energetically efficient modes of locomotion to increase surfacing behavior efficiency, suggesting the hydro-physical environment as a major determinant of river cetaceans distribution and abundance. Flow and AWS relationships indicate that the flow during dry season negatively contributed to AWS, whereas that of pre-monsoon maximized the AWS, suggesting that modifying flow regimes does alter in-stream habitats at varying spatial scales and may influence life-history strategies. Substantial fragmentation in suitable pool availability and loss of longitudinal connectivity exhibited by dry season flow suggested a higher risk of adverse biological effects during the dry season, which may reduce population viability by reducing survivorship and reproduction failure. Owing to riverine cetaceans dependence on the attribute of freshwater flow, they can be expected to be more affected by flow regulations as interactive effects. Considering the seasonal effects and changes in the availability of usable areas by flow alteration, adopting effective habitat retention plans by water-based development projects appears critical to avoid further ecological risks in aquatic species conservation. Identifying priority riverscapes for river cetaceans and prioritizing investment opportunities is an essential first step towards effective riverine cetacean conservation.

ecology↗
bioRxiv2020

Inferring species interactions from ecological survey data: a mechanistic approach to predict quantitative food webs of seed-feeding by carabid beetles

O_LIEcological networks are valuable for ecosystem analysis but their use is often limited by a lack of data because many types of ecological interaction, e.g. predation, are short-lived and difficult to observe or detect. There are different methods for inferring the presence of interactions, which we lack methods to predict interaction strengths and so use weighted network analysis. C_LIO_LIHere, we develop a trait-based approach suitable for creating quantitative networks, i.e. with varying interaction strengths. We developed the method for seed-feeding carabid ground beetles (Coleoptera: Carabidae) although the principles can be applied to other interactions. C_LIO_LIWe used existing literature data from experimental seed-feeding trials to predict a per-individual interaction cost index based on carabid and seed size with frequency-dependent prey selection and assuming bottom up control. This was scaled up to the population level to create predicted inferred weighted networks using the abundance of carabids and seeds in samples from arable fields and energetic intake rates of carabids from the literature. From these weighted networks, we also calculated a novel measure of predation pressure. C_LIO_LIWe applied it to existing ecological survey data from 255 arable fields with carabid data from pitfall traps and plant seeds from seed rain traps. Analysis of these inferred networks led to testable hypotheses about how networks and predation pressure varied amongst fields. C_LIO_LIInferred networks are valuable because (i) they provide null models for the structuring of food webs to test against empirical species interaction data, e.g. DNA analysis of carabid gut regurgitates, and (ii) they allow weighted inferred networks to be constructed whenever we can estimate interactions between species and have ecological census data available. This would permit network analysis even at times and in places when interactions were not directly assessed. C_LI

ecology↗
bioRxiv2020

Cheese or cheese infusions - Ecological traps for mosquitoes and spotted wing Drosophila

We tested the hypothesis that the "ecological trap" phenomenon (a mismatch between a habitats perceived attractiveness and its actual quality, resulting in a population sink) is exploitable for pest control. We selected mosquitoes as modal organisms, because selection of an oviposition site by adult female mosquitoes in response to its perceived attractiveness is of paramount importance for the development and survival of their larval offspring. In laboratory and/or field experiments, we show that (i) each of five cheese varieties tested (Raclette, Pecorino, Brie, Gruyere, Limburger) strongly attracts females of both the yellow fever mosquito, Aedes aegypti, and the common house mosquito, Cx. pipiens; (ii) cheese infusions, or headspace odorant extracts (HOEs) of cheese infusions, significantly affect oviposition choices by Cx. pipiens and Ae. aegypti, (iii) HOEs contain at least 13 odorants; (iv) in field settings, cheese infusions more effectively stimulate oviposition by Cx. pipiens and Culiseta incidens than bluegrass (Poa sp.) infusions, and also capture (by drowning) the spotted wing Drosophila (SWD); (v) the microbe composition of home-made cheese infusions modulates oviposition choices by mosquitoes; and (vi) the type of cheese infusion coupled with its nutritional content strongly affects the survivorship of mosquito larvae. In combination, our data show that microbial metabolites associated with cheese and cheese infusions are both attractive to adult mosquitoes seeking hosts and oviposition sites, respectively, and are toxic to mosquito larvae. These microbes and their metabolites could thus be coopted for both the attract and the kill function of "attract & kill" mosquito control tactics. Implementation of customizable and non-conventional nutritional media, such as home-made cheese infusions, as microbe-based ecological traps presents a promising concept which exploits insect ecology for insect control.

ecology↗
bioRxiv2021

Data proliferation, reconciliation, and synthesis in viral ecology

The fields of viral ecology and evolution have rapidly expanded in the last two decades, driven by technological improvements, and motivated by efforts to discover potentially zoonotic wildlife viruses under the rubric of pandemic prevention. One consequence has been a massive proliferation of host-virus association data, which comprise the backbone of research in viral macroecology and zoonotic risk prediction. These data remain fragmented across numerous data portals and projects, each with their own scope, structure, and reporting standards. Here, we propose that synthesis of host-virus association data is a central challenge to improve our understanding of the global virome and develop foundational theory in viral ecology. To illustrate this, we build an open reconciled mammal-virus database from four key published datasets, applying a standardized taxonomy and metadata. We show that reconciling these datasets provides a substantially richer view of the mammal virome than that offered by any one individual database. We argue for a shift in best practice towards the incremental development and use of synthetic datasets in viral ecology research, both to improve comparability and replicability across studies, and to facilitate future efforts to use machine learning to predict the structure and dynamics of the global virome.

ecology↗