Tag: Ecological Networks

Ecology

Merging dietary metabarcoding into networks: turning “don’ts” into “dos”

Post provided by Jordan Cuff, Fredric Windsor, Maximillian Tercel, James Kitson and Darren Evans.

Do you spend your days incapacitated by the agony of not knowing how to combine your field-based observational data with your dietary metabarcoding results? Perhaps every time you go to merge them, the horror of conflicting data types and biases causes you to run and hide from the mere thought of analysis. Or maybe the thought of such problems hadn’t even crossed your mind! In this post, Jordan Cuff and co-authors share insight from their recent publication on using dietary metabarcoding in network ecology and how to merge metabarcoding with traditional data types.

Continue reading “Merging dietary metabarcoding into networks: turning “don’ts” into “dos””
Unknown's avatarBen Whittaker1 Comment
Robert May Prize

The quest for a sharp definition of function in biological networks

Robert May Prize Shortlisted Article

Post provided by Alberto Pascual-García

Credit: Pascual & Bell 2020

Each year Methods in Ecology and Evolution awards the Robert May Prize to the best paper in the journal by an author at the start of their career. Alberto Pascual has been shortlisted for his article ‘functionInk: An efficient method to detect functional groups in multidimensional networks reveals the hidden structure of ecological communities’. In this post, Alberto discusses the application of the functionInk (functional linkage) package for distinguishing modules and guilds from large multidimensional networks.

Continue reading “The quest for a sharp definition of function in biological networks”
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Methods papers, Robert May Prize, Statistical methods

Species association networks: a bridge between sciences

Robert May Prize Shortlisted Article

Post provided by Raphaëlle Momal

Powdery mildew on oak tree leaves is caused by the fungi Erysiphe alphitoides, which association network helps understanding the behaviour. Credit: Raphaëlle Momal.

Each year Methods in Ecology and Evolution awards the Robert May Prize to the best paper in the journal by an author at the start of their career. Raphaëlle Momal has been shortlisted for her article ‘Tree‐based inference of species interaction networks from abundance data’. In this blog, Raphaëlle discusses how her paper came to be and the applications of the R package developed in her study.

Continue reading “Species association networks: a bridge between sciences”
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International Days

World Wetlands Day: Wetlands and Water

Post provided by Chloe Robinson

World Wetlands Day 2021 shines a spotlight on wetlands as a source of freshwater and encourages actions to restore them and stop their loss. Credit: Ramsar.org.

It doesn’t come as a surprise that healthy wetland systems are linked with freshwater quality. Wetlands form vital habitats for global biodiversity, help combat climate change through storage of carbon and offer defenses against flooding. Freshwater resources, including wetlands, are under increasing pressure from over-abstraction, pollution and habitat destruction among other threats, which is directly contributing to the current global freshwater crisis that threatens people and our planet.

February 2nd each year is World Wetlands Day, which aims to raise global awareness about the vital role of wetlands. This year, the 2021 campaign highlights the contribution of wetlands to the quantity and quality of freshwater on our planet. Water and wetlands are connected in an inseparable co-existence that is vital to life, our well-being, and the health of our planet. In this blog post, Associate Editor Chloe Robinson, will explore why wetlands are so important and the new DNA-based methods being used to monitor wetland health.

Continue reading “World Wetlands Day: Wetlands and Water”
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General

Influential Women in Ecological Network Research

Post provided by Katherine Baldock and Luísa G. Carvalheiro

luisa-carvalheiro-butterfly
©Luísa G. Carvalheiro

Ecological networks represent interactions between different biotic units in an ecosystem and are becoming an increasingly popular tool for describing and illustrating a range of different types of ecological interactions. Food webs – which provide a way to track and quantify the flow of energy and resources in ecosystems – are among the most studied type of ecological networks. These networks usually represent species (nodes) which are connected by pairwise interactions (links) and they play a central role in improving our understanding of ecological and evolutionary dynamics.

Historically, food webs described antagonistic relationships (e.g. plant-herbivore or host-parasitoid networks) but the approach has been developed in recent years to include mutualistic networks (e.g. plant-pollinator networks, phorophyte-epiphyte networks). The development of network ecology, including ever more sophisticated methods to analyse ecological communities, has been driven forward by an enthusiastic community of ecologists, theoreticians and modellers working together to enhance our understanding of how communities interact.

In this blog post, we’ll describe the important role played by female scientists in the development of network ecology, focusing on the contributions by two ground-breaking ecologists and also highlighting contributions from a range of other scientists working in this field. Continue reading “Influential Women in Ecological Network Research”

Unknown's avatarIndia StephensonLeave a comment
Journal updates, Methods papers

Issue 7.2: Demography Beyond the Population

Issue 7.2 is now online!

Sagebrush steppe in eastern Idaho, USA
© Brittany J. Teller

The February issue of Methods is now online! As you may have seen already, it includes the BES cross-journal Special Feature: “Demography Beyond the Population“. There are also eight other wonderful articles to read.

We have four articles in the Demography Beyond the Symposium Special Feature. You can read an overview of them by two of the Feature’s Guest Editor Sean McMahon and Jessica Metcalf here (Sean and Jessica are also Associate Editors of Methods).

If you’d like to find out more about each of the individual papers before downloading them, we have blog posts about each one. Daniel Falster and Rich Fitzjohn discuss the development of plant and provide some advice on creating simulation models in Key Technologies Used to Build the plant Package (and Maybe Soon Some Other Big Simulation Models in R). There is a look back at the evolution of Integral Projection Models from Mark Rees and Steve Ellner in How Did We Get Here From There? A Brief History of Evolving Integral Projection Models. In Inverse Modelling and IPMs: Estimating Processes from Incomplete Information Edgar González explains how you can estimate process that you can’t observe. And keep an eye out for Brittany Teller’s blog post coming next week!

Don’t wait too long to get the Demography Beyond the Population Special Feature papers though, they’re freely available for a limited time only

Continue reading “Issue 7.2: Demography Beyond the Population”

Unknown's avatarIndia StephensonLeave a comment
Journal updates, Methods papers

Issue 7.1

Issue 7.1 is now online!

The January issue of Methods is now online!

As always, the first issue of the year is our sample issue. You can access all of the articles online free of charge. No subscription or membership is required!

We have two Open Access articles and two Applications papers in our January issue.

– Recognizing False Positives: Environmental DNA (eDNA) is increasingly used for surveillance and detection of species of interest in aquatic and soil samples. A significant risk associated with eDNA methods is potential false-positive results due to laboratory contamination. To minimize and quantify this risk, Chris Wilson et al. designed and validated a set of synthetic oligonucleotides for use as species-specific positive PCR controls for several high-profile aquatic invasive species.

– BiMat: An open-source MATLAB package for the study of the structure of bipartite ecological networks. BiMat enables both multiscale analysis of the structure of a bipartite ecological network – spanning global (i.e. entire network) to local (i.e. module-level) scales – and meta-analyses of many bipartite networks simultaneously. The authors have chosen to make this Applications article Open Access.

Gemma Murray et al. provide this month’s second Open Access article. In ‘The effect of genetic structure on molecular dating and tests for temporal signal‘ the authors use simulated data to investigate the performance of several tests of temporal signal, including some recently suggested modifications. The article shows that all of the standard tests of temporal signal are seriously misleading for data where temporal and genetic structures are confounded (i.e. where closely related sequences are more likely to have been sampled at similar times). This is not an artifact of genetic structure or tree shape per se, and can arise even when sequences have measurably evolved during the sampling period.

Our January issue also features articles on Monitoring, Population Ecology, Genetics, Evolution, Community Ecology, Diversity and more. Continue reading “Issue 7.1”

Unknown's avatarIndia StephensonLeave a comment
Journal updates, Methods papers

A new tool based on microbial interactions to analyze bipartite networks

Below is a press release about the Methods paper ‘BiMat: a MATLAB package to facilitate the analysis of bipartite networks‘ taken from the Pompeu Fabra University.

The Georgia Institute of Technology has created, together with the Pompeu Fabra University and the University of Canterbury, a new open-access and open-source tool for the study of bipartite networks

The team led by Joshua S. Weitz, Associate Professor at the School of Biology from the Georgia Institute of Technology, has developed BiMat: an open source MATLAB® package for the study of the structure of bipartite ecological networks inspired by real problems in microbiology and with broader applications. Cesar O. Flores, researcher at the School of Physics of the same institute, describes this new tool in an article published in the journal Methods in Ecology and Evolution. Sergi Valverde, Visiting Professor at the Complex Systems Lab from the Pompeu Fabra University, and Timothée Poisot, from the School of Biological Sciences of the University of Canterbury, are involved in the project. Continue reading “A new tool based on microbial interactions to analyze bipartite networks”

Unknown's avatarIndia StephensonLeave a comment
Methods papers, Online extras

National Honey Bee Day 2015

Happy National Honey Bee Day everyone!

As you may know, tomorrow (Saturday 22 August) is National Honey Bee Day in the USA. To mark the day we will be highlighting some of the best papers that have been published on bees and pollinators in Methods in Ecology and Evolution.

You can find out more about National Honey Bee Day (and about bees in general) HERE.

Without further ado though, here are a few of the best Methods papers related to Honey Bees:

Wildebeast graze on the cover of MEE 2.5Honey Bee Risk Assessment

Our Honey Bee highlights begin with Hendriksma et al.’s article ‘Honey bee risk assessment: new approaches for in vitro larvae rearing and data analyses‘. Robust laboratory methods for assessing adverse effects on honey bee brood are required for research into the issues contributing to global bee losses. To facilitate this, the authors of this article recommend in vitro rearing of larvae and suggest some appropriate statistical tools for the related data analyses. Together these methods can help to improve the quality of environmental risk assessment studies on honey bees and secure honey bee pollination. As this article was published over two years ago, it can be accessed for free by anyone.

Continue reading “National Honey Bee Day 2015”

Unknown's avatarIndia Stephenson3 Comments
Journal updates, Methods papers

Issue 6.8

Issue 6.8 is now online!

The August issue of Methods is now online!

This month’s issue contains two Applications article and one Open Access article, all of which are freely available.

– LEA: This R package enables users to run ecological association studies from the R command line. It can perform analyses of population structure and genome scans for adaptive alleles from large genomic data sets. The package derives advantages from R programming functionalities to adjust significance values for multiple testing issues and to visualize results.

– PIPITS: An open-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables.

Giovanni Strona and Joseph Veech provide this month’s Open Access article. Many studies have focused on nestedness, a pattern reflecting the tendency of network nodes to share interaction partners, as a method of measuring the structure of ecological networks. In ‘A new measure of ecological network structure based on node overlap and segregation‘ the authors introduce a new statistical procedure to measure both this kind of structure and the opposite one (i.e. species’ tendency against sharing interacting partners).

In addition to this, our August issue features articles on Estimating Diversity, Ecological Communities and Networks, Genetic Distances and Immunology. Continue reading “Issue 6.8”

Unknown's avatarIndia StephensonLeave a comment