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:
Honey 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.
On Friday, we gave some more information about the research articles in this Virtual Issue. In this post, we will be focusing on the Applications papers.
Applications papers introduce new tools for research, which provide practitioners with an important source of information and background on the tools they use. In this Virtual Issue we have highlighted the newest Applications papers that describe how phylogenetic methods are contributing to the fields of ecology and evolution. These include tools with aims as diverse as phylogenetic tree reconstruction and analysing phylogenetic diversity in communities. All Applications papers, not just those in the Virtual Issue, are free to access.
You can see a little more information on each of the Applications Papers below.
An understanding of the tree of life contributes to many facets of biology. This Virtual Issue has assembled studies that showcase the breadth of the utility of phylogenetic trees, including phylogenetic beta diversity, trait evolution, diversification, biodiversity studies, phylogenetic signal, biogeography, ecosystem functioning, and host-pathogen dynamics.
The Research papers included are excellent examples of new ways that phylogenies can be applied to central questions in ecology, evolution and biodiversity, such as measuring niche conservatism, trait evolution and diversification rates. The issue also has articles on barcoding methods, which increasingly are used to understand phylogenetic and functional diversity.
You can see a little more information on each of the articles below.
As you may know, today (Friday 22 May) is the United Nations Day for Biodiversity and we are celebrating by highlighting some of the best papers that have been published on biodiversity in Methods in Ecology and Evolution. This is by no means an exhaustive list and you can find many more articles on similar topics on the Wiley Online Library (remember, if you are a member of the BES, you can access all Methods articles free of charge).
If you would like to learn more about the International Day for Biological Diversity, you may wish to visit the Convention on Biological Diversity website, follow them on Twitter or check out today’s hashtag: #IBD2015.
Without further ado though, here are a few of the best Methods papers on Biological Diversity:
We begin with an Open Access article from one of our Associate Editors, Douglas Yu (et al.). This article was published in the August issue of 2012 and focuses on the metabarcoding of arthropods. The authors present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. They also demonstrate that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information.
Today, biological invasions are of major concern for maintaining biodiversity. However, understanding what drives the success of invasive species at the scale of the community remains a challenge. Two processes have been described as main drivers of the coexistence between invasive and native species: environmental filtering and competitive interactions. However, recent reviews have shown that competitive interactions are rarely detected, and thus their importance as drivers of invasion success placed under question. But can this be due to pure methodological issues? Using a simulation model of community assembly, Laure and co-authors (Marta Carboni and Tamara Münkemüller) show that the infrequent detection of competition can arise from three important methodological shortcomings, and provide guidelines for future studies of invasion drivers at the scale of the community.
A Beginner’s Guide to Data Exploration and Visualisation with R by Elena N. Ieno and Alain F. Zuur
In 2010 Alain Zuur, Elena Ieno and Chris Elphick published a paper in Methods in Ecology and Evolution entitled ‘A protocol for data exploration to avoid common statistical problems‘ (Volume 1, Issue 1). Little did they know at the time that this paper would become one of the journal’s all-time top downloaded and top cited papers, with a total of 22,472 downloads between 2010 and 2014.
Based on this success they decided to extend the material in the paper into a book.
Zuur and his colleagues at Highland Statistics ltd. give about 25 five-day statistics courses per year. Their typical audience consists of biological scientists at the post-graduate and post-doctoral levels. Early on in each course they have the following conversation with the participants:
Speaker: “Do you review submitted manuscripts for journals?” Audience: “Yes.” Speaker: “Do you like the statistical part of these manuscripts?” Audience: “No!” Speaker: “Do you understand the statistical part?” Audience: “Not always.”
What if there were ways you could make reviewing your paper easier and more enjoyable for reviewers? What if making your manuscript easier to understand and nicer to read would increase the likelihood of your work being published?
A Beginner’s Guide to Data Exploration and Visualisation with R explains how you can do exactly that! Alain Zuur and Elena Ieno use ecological datasets to discuss the data exploration and visualisation tools you can use to make your paper simpler for readers and reviewers to understand. The authors also explain how to visualise the results of statistical models, an important aspect of scientific papers. Continue reading →
What links tea bags, glove puppets, vandalism, and cheddar? Or catching birds, bug soup, criminal profiling, snow leopards and jaguars? Methods in Ecology and Evolution, obviously! We have now been publishing new methods for over 4 years, and the sheer variety of papers we have received is quite amazing: field, lab, statistics, simulations and computing. All areas of methodology have been covered, as have all areas of ecology and evolution: evolutionary biology, population genetics, conservation, stable isotopes, plant ecology, simulation modelling…the variety is almost overwhelming! In this Virtual Issue we have collated some of the most popular papers that we have published over the past four years, to showcase their high quality and diversity.
Our applications papers are always free, and all papers are free after 2 years; in addition all papers are completely free for BES members. So if you don’t have access already, why not join the BES, and along with all of the membership benefits you will get free access to MEE as a bonus?
Our editors and I will be attending some of the major ecology and evolution conferences this summer – so look out for us and do say hi!
Although ecologists frequently want to make use of phylogenies, they often lack the skills to create detailed phylogenies of their study taxa. phyloGenerator greatly simplifies the process of creating a phylogeny, automating the download of DNA data and the use of modern phylogenetic software to produce a dated, defensible phylogeny. By linking together a number of existing tools into a single command-line interface and providing an extendable Python library, phyloGenerator is also a useful tool for phylogeneticists wishing to use an open, reproducible phylogenetic workflow. The Editors commented that, “this is an exciting idea that makes phylogenies almost immediately accessible to any researcher needing to use them. It is also a terrific example of the power of what we can achieve when data are made open and accessible.”
Will studied Zoology as an undergraduate at the University of Cambridge, then completed an MSc in Ecology, Evolution and Conservation, and later a PhD at Imperial College London supervised by Andy Purvis and David Roy (Centre for Ecology and Hydrology, Wallingford). His PhD focused on how the phylogeny of species in a community can be used to understand the ecological assembly of that community, and how phylogeny informs our understanding of communities undergoing change. Will is now a post-doc in Jeannine Cavender-Bares’ lab at the University of Minnesota, where he studies urban plant communities.
The Robert May Prize is awarded annually to the best paper published in Methods by a young author at the start of their research career. We’re delighted to announce that the 2012 winner is Sarah Papworth from Imperial Collage London, for her article “Movement ecology of human resource users: using net squared displacement, biased random bridges and resource utilization functions to quantify hunter and gatherer behaviour”. Although GPS trackers can rapidly collect vast amounts of data on animal movement, appropriate methods for analysing this data are still being developed. The paper describes a methodological framework for the analysis of GPS track records of foragers which routinely return to a central place after foraging, such as a den or nest. The framework combines three existing methods in a flexible method for the accurate description of resource use and movement in humans and animals. This approach will be particularly useful for our understanding of human resource extraction and conservation planning.
Sarah studied a BA Honours in Anthropology at the University of Durham, which focused on human and primate behaviour. This lead to an interest in field biology in the tropics, and she went on to study blue monkeys in Uganda. She then completed an MSc in Ecology, Evolution and Conservation, and a PhD in Conservation Science, at Imperial College London, supervised by E.J. Milner-Gulland and Katie Slocombe (University of York). Her PhD focused on human and primate behaviour within the context of hunting by the Waorani of Amazonian Ecuador, and involved extensive fieldwork. Data collected for her PhD were used to illustrate the methodological framework developed in the Robert M. May prize-winning paper. She has just moved to Singapore, where she is currently a research fellow focusing on poverty and biodiversity at the National University of Singapore.
The above 3 articles will be included in a free virtual issue this year, along with all of the winning and short-listed articles from the other 4 British Ecological Society journals young investigator prizes.