scholarly journals Sampling networks of ecological interactions

2015 ◽  
Author(s):  
Pedro Jordano
Keyword(s):  
Sampling Effort ◽  
Ecological Interactions ◽  
Formal Approach ◽  
Sampling Protocols ◽  
Biodiversity Inventories ◽  
Adequate Sampling ◽  
Potential Interactions ◽  
Sizable Fraction ◽  
Interspecific Encounter

1. Sampling 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. 2. Robust 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. 3. While 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 I_{max among, say, A animal species and P plant species (i.e., I_max= 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<<I_{max}, resulting in extremely sparse interaction matrices with low connectance. 4. Reasons 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. Adequately assessing the completeness of a network of ecological interactions thus needs knowledge of the natural history details embedded, so that forbidden links can be "discounted'' when addressing sampling effort. 5. Here 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.

scholarly journals Formal Modeling and Analysis of Fairness Characterization of E-Commerce Protocols

2014 ◽  
Vol 2014 ◽  
pp. 1-10
Author(s):  
Chengwei Zhang ◽  
Xiaohong Li ◽  
Jing Hu ◽  
Zhiyong Feng ◽  
Jiaojiao Song
Keyword(s):  
Formal Modeling ◽  
Sufficient Condition ◽  
Formal Approach ◽  
Common Assumption ◽  
Modeling And Analysis ◽  
Verification Method ◽  
Space Model ◽  
The Past

In the past, fairness verification of exchanges between the traders in E-commerce was based on a common assumption, so-called nonrepudiation property, which says that if the parties involved can deny that they have received or sent some information, then the exchanging protocol is unfair. So, the nonrepudiation property is not a sufficient condition. In this paper, we formulate a new notion of fairness verification based on the strand space model and propose a method for fairness verification, which can potentially determine whether evidences have been forged in transactions. We first present an innovative formal approach not to depend on nonrepudiation, and then establish a relative trader model and extend the strand space model in accordance with traders’ behaviors of E-commerce. We present a case study to demonstrate the effectiveness of our verification method.

scholarly journals Interactions among ecosystem stressors and their importance in conservation

2016 ◽  
Vol 283 (1824) ◽  
pp. 20152592 ◽  
Author(s):  
Isabelle M. Côté ◽  
Emily S. Darling ◽  
Christopher J. Brown
Keyword(s):  
Biological Processes ◽  
Additive Effects ◽  
Ecological Interactions ◽  
The Past ◽  
Ecological Literature ◽  
Adaptive Monitoring ◽  
Ecosystem Stressors ◽  
Meta Analyses ◽  
Potential Interactions ◽  
Near Future

Interactions between multiple ecosystem stressors are expected to jeopardize biological processes, functions and biodiversity. The scientific community has declared stressor interactions—notably synergies—a key issue for conservation and management. Here, we review ecological literature over the past four decades to evaluate trends in the reporting of ecological interactions (synergies, antagonisms and additive effects) and highlight the implications and importance to conservation. Despite increasing popularity, and ever-finer terminologies, we find that synergies are (still) not the most prevalent type of interaction, and that conservation practitioners need to appreciate and manage for all interaction outcomes, including antagonistic and additive effects. However, it will not be possible to identify the effect of every interaction on every organism's physiology and every ecosystem function because the number of stressors, and their potential interactions, are growing rapidly. Predicting the type of interactions may be possible in the near-future, using meta-analyses, conservation-oriented experiments and adaptive monitoring. Pending a general framework for predicting interactions, conservation management should enact interventions that are robust to uncertainty in interaction type and that continue to bolster biological resilience in a stressful world.

scholarly journals The Poisson-Lognormal Model as a Versatile Framework for the Joint Analysis of Species Abundances

2021 ◽  
Vol 9 ◽  
Author(s):  
Julien Chiquet ◽  
Mahendra Mariadassou ◽  
Stéphane Robin
Keyword(s):  
Species Distribution Models ◽  
Habitat Type ◽  
Joint Analysis ◽  
Species Competition ◽  
Ecological Interactions ◽  
Distribution Models ◽  
Variational Techniques ◽  
Species Abundances ◽  
Potential Interactions ◽  
Multivariate Sample

Joint Species Distribution Models (JSDM) provide a general multivariate framework to study the joint abundances of all species from a community. JSDM account for both structuring factors (environmental characteristics or gradients, such as habitat type or nutrient availability) and potential interactions between the species (competition, mutualism, parasitism, etc.), which is instrumental in disentangling meaningful ecological interactions from mere statistical associations. Modeling the dependency between the species is challenging because of the count-valued nature of abundance data and most JSDM rely on Gaussian latent layer to encode the dependencies between species in a covariance matrix. The multivariate Poisson-lognormal (PLN) model is one such model, which can be viewed as a multivariate mixed Poisson regression model. Inferring such models raises both statistical and computational issues, many of which were solved in recent contributions using variational techniques and convex optimization tools. The PLN model turns out to be a versatile framework, within which a variety of analyses can be performed, including multivariate sample comparison, clustering of sites or samples, dimension reduction (ordination) for visualization purposes, or inferring interaction networks. This paper presents the general PLN framework and illustrates its use on a series a typical experimental datasets. All the models and methods are implemented in the R package PLNmodels, available from cran.r-project.org.

scholarly journals A section-sampling design to assess zooplankton distribution in a highly complex hydrographic region (SW Atlantic Ocean, 34-41ºS): insights for a new time series?

2012 ◽  
Vol 60 (3) ◽  
pp. 381-390 ◽  
Author(s):  
Georgina Daniela Cepeda ◽  
Rosana Di Mauro ◽  
Patricia Martos ◽  
Maria Delia Viñas
Keyword(s):  
Time Series ◽  
Sampling Design ◽  
Stock Assessment ◽  
Fish Stock ◽  
Sampling Effort ◽  
Zooplankton Distribution ◽  
Data Platform ◽  
Adequate Sampling ◽  
Sw Atlantic ◽  
Fish Stock Assessment

Regular fish stock assessment cruises could provide a proper data platform to sample zooplankton. It is essential, however, that adequate sampling designs should be developed for each area so that zooplankton features may be accurately described with minimum sampling effort. On the Northern Argentine Continental Shelf (NACS, 34-41ºS), a sectioned-sampling design (18 samples distributed in 4 sections) associated with E. anchoita stock estimation cruises was implemented to provide a rapid and reliable survey of zooplankton distribution in relation to the physical environment. The results obtained were similar to those registered in previous studies based on exhaustive sampling. We suggest that a new zooplankton time series covering this broad área be established, based on this sampling design, to contribute to the knowledge of the variability of zooplankton populations and their relation to fishery resources.

Optimising design and effort for environmental surveys using dung beetles (Coleoptera: Scarabaeidae)

2016 ◽  
Vol 149 (2) ◽  
pp. 214-226 ◽  
Author(s):  
Claudia Tocco ◽  
Danielle E.A. Quinn ◽  
John M. Midgley ◽  
Martin H. Villet
Keyword(s):  
Sampling Method ◽  
Ground Level ◽  
Dung Beetle ◽  
Pitfall Trap ◽  
Dung Beetles ◽  
Sampling Effort ◽  
Eastern Cape ◽  
Trap Design ◽  
Sampling Protocols ◽  
By Catch

AbstractIn biological monitoring, deploying an effective standardised quantitative sampling method, optimised by trap design and sampling effort, is an essential consideration. To exemplify this using dung beetle (Coleoptera: Scarabaeidae: Scarabaeinae and Aphodiinae) communities, three pitfall trap designs (un-baited (TN), baited at ground level (flat trap, TF), and baited above the trap (hanging trap, TH)), employed with varying levels of sampling effort (number of traps=1, 2, 3 … 10; number of days=1, 2, 3), were evaluated for sampling completeness and efficiency in the Eastern Cape, South Africa. Modelling and resampling simulation approaches were used to suggest optimal sampling protocols across environmentally diverse sites. Overall, TF recovered the greatest abundance and species richness of dung beetles, but behavioural guilds showed conflicting trends: endocoprids preferred TH while paracoprids and telocoprids preferred TF. Resampling simulation of trap type and the two components of sampling effort suggested that six TF traps left for three days was most efficient in obtaining a representative sample and allowed differentiation between trap types, allowing the improved efficiency to be recognised. The effect of trap type on non-target specimens, particularly ants, was also investigated. TF and TH caught almost no by-catch, which is ethically desirable.

scholarly journals National Institute on Aging Workshop: Repurposing Drugs or Dietary Supplements for Their Senolytic or Senomorphic Effects: Considerations for Clinical Trials

2021 ◽  
Author(s):  
Sergei Romashkan ◽  
Henry Chang ◽  
Evan C Hadley
Keyword(s):  
Dietary Supplements ◽  
Cell Types ◽  
Small Scale ◽  
Phase Ii Trials ◽  
Cytotoxic Effects ◽  
Standardized Measures ◽  
Age Related ◽  
Secretory Phenotype ◽  
Potential Interactions

Abstract Background Cell senescence is implicated in numerous age-related conditions. Drugs and nutritional supplements developed for a variety of purposes kill senescent cells (senolytics) or suppress their secretions (senomorphics). There is interest in repurposing such drugs to treat or prevent age-related diseases. To date, only small-scale preliminary trials have been conducted. Method At a workshop convened by the National Institute on Aging in August 2019, academic, industry, and government scientists reviewed issues for phase II trials of potentially repurposable drugs, or dietary supplements, to assess benefits and risks of their senolytic (killing senescent cells) or senomorphic (altering senescent cells’ phenotypes) effects in treating or preventing age-related conditions. Results Participants reviewed mechanisms and effects of cellular senescence, senolytics, and senomorphics of several classes and their potential role in treating or preventing disease, modulators of the senescence-associated secretory phenotype, needs for senescence markers, data and specimen resources, infrastructure for planning trials, and potential effects on outcomes in older patients with multimorbidity and polypharmacy. Conclusions Participants noted the importance of considering potential effects of candidate drugs on multiple aging outcomes. It is important to assess drugs’ specificity for killing senescent cells and the balance between senolytic and cytotoxic effects. Markers of specific senescent cell types are needed to assess intervention responses. There are potential interactions with coexisting diseases and their treatments in older persons. Standardized measures could enhance comparisons and pooling of data. Additional characterization of human cell senescent phenotypes is needed for developing better and more specific senolytics and senomorphics.

scholarly journals Revealing biases in the sampling of ecological interaction networks

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7566 ◽  
Author(s):  
Marcus A.M. de Aguiar ◽  
Erica A. Newman ◽  
Mathias M. Pires ◽  
Justin D. Yeakel ◽  
Carl Boettiger ◽  
...  
Keyword(s):  
Large Scale ◽  
Sampling Design ◽  
Species Interaction ◽  
Ecological Networks ◽  
Interaction Networks ◽  
Sampling Effort ◽  
Large Species ◽  
Ecological Interactions ◽  
Underlying Network ◽  
High Degree

The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases with respect to 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 ecological and statistical issues directly affect ecologists’ abilities to accurately construct ecological networks. However, statistical biases introduced by sampling are difficult to quantify in the absence of full knowledge of the underlying ecological network’s structure. To explore properties of large-scale ecological networks, we developed the software 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 mathematical sampling designs that correspond to methods used 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 depends strongly 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, modules with nested structure were the easiest to detect, regardless of the sampling design used. Sampling a network starting with any species that had a high degree (e.g., abundant generalist species) was consistently found to be the most accurate strategy to estimate network structure. Because high-degree species tend to be generalists, abundant in natural communities relative to specialists, and connected to each other, sampling by degree may therefore be common but unintentional in empirical sampling of networks. 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. To reduce biases introduced by sampling methods, we recommend that these findings be incorporated into field design considerations for projects aiming to characterize large species interaction networks.

scholarly journals An Implementation Approach for the Humboldt Extension to Darwin Core

2021 ◽  
Vol 5 ◽  
Author(s):  
Peter Brenton
Keyword(s):  
Species Abundance ◽  
Practical Implementation ◽  
Sampling Effort ◽  
Darwin Core ◽  
Implementation Approach ◽  
Sampling Protocols ◽  
Field Data Collection ◽  
Event Based ◽  
Temporal Coverage ◽  
Occurrence Records

The Humboldt extension to the Darwin Core Standard Event Core has been proposed in order to provide a standard framework to capture important information about the context in which biodiversity occurrence observations and samples are recorded. This information includes methods and effort, which are critical for determining species abundance and other measures of population dynamics, as well as completeness of survey coverage. As this set of terms is being developed, we are using real-world use cases to ensure that these terms can address all known situations. We are also considering approaches to implementation of the new standard to maximise opportunities for uptake and adoption. In this presentation I provide an example of how the Humboldt extension will be implemented in the Atlas of Living Australia’s (ALA) BioCollect application. BioCollect is a cloud-based multi-project platform for all types of biodiversity and ecological field data collection and is particularly suited for capturing fully described complex protocol-based systematic surveys. For example, BioCollect supports a wide array of customised survey event-based data schemas, which can be configured for different kinds of stratified (and other) sampling protocols. These schemas can record sampling effort at the event level and event effort can be aggregated across a dataset to provide a calculated measure of effort based on the whole dataset. Such data-driven approaches to providing useful dataset-level metadata can also be applied to measures of taxonomic completeness as well as spatial and temporal coverage. In addition, BioCollect automatically parses biodiversity occurrence records from event records for harvest by the ALA. In this process, the semantic relationship between the occurrence records and their respective event records is also preserved and linkages between them enable cross-navigation for improved contextual interpretation. The BioCollect application demonstrates one approach to a practical implementation of the Humboldt extension.

scholarly journals Diversity and Altitudinal Distribution of Understorey Corticolous Lichens in a Tropical Montane Forest in Kenya (East Africa)

2018 ◽  
Author(s):  
Paul M. Kirika ◽  
George G. Ndiritu ◽  
George K. Mugambi ◽  
Leonard E. Newton ◽  
H. Thorsten Lumbsch
Keyword(s):  
East Africa ◽  
Structural Heterogeneity ◽  
Climatic Conditions ◽  
Windward Side ◽  
Leeward Side ◽  
Sampling Effort ◽  
Forest Types ◽  
Altitudinal Distribution ◽  
Adequate Sampling ◽  
Study Sites

Lichens constitute an important component of tropical forest biodiversity. This study inventoried corticolous lichens and examined their variation in various forest types with varying climatic conditions in Mt. Kenya, East Africa. Specifically we evaluated variation of lichen assemblages in relation to forest types and tree diversity along an altitudinal gradient (1800-3100m). Ten study sites were established on two contrasting sides of Mt. Kenya in the indigenous forest: six of them at Chogoria which is on the humid southeastern windward side of the mountain and four sites on the Sirimon side located on the drier northwestern leeward side. Overall 242 lichen taxa were documented; with Chogoria and Sirimon forests having 148 and 94 species that translated to an adequate sampling effort of 74 % and 68 %, respectively. The two contrasting forest types (Chogoria and Sirimon) supported slightly different lichens assemblages. Meanwhile lichen assemblages were found to significantly vary with elevation (or forest types) and with tree host. Posterior analyses showed that the differences were significant among sampling sites (or forest types) on the Chogoria side and insignificant on the Sirimon side. Similarly the number of lichens differed significantly among the host tree species. This study stresses the urgent need to upscale the sustainable management of the presently threatened tropical forests in order to preserve their structural heterogeneity.

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