The September issue of Methods is now online!

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

– POPART: An integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. The package also provides a platform for the implementation and distribution of new network-based methods.

Michalis Vardakis et al. provide this month’s first Open Access article. In ‘Discrete choice modelling of natal dispersal: ‘Choosing’ where to breed from a finite set of available areas‘ the authors show how the dispersal discrete choice model can be used for analysing natal dispersal data in patchy environments given that the natal and the breeding area of the disperser are observed. This model can be used for any species or system that uses some form of discrete breeding location or a certain degree of discretization can be applied.

Our September issue also features articles on Animal Movement, Population Dynamics, Statistical Ecology, Biodiversity, Conservation Biology and much more.

This issue also contains an article which was accompanied by one of our most popular blog posts this year. In ‘Comparing methods to separate components of beta diversity‘ Andrés Baselga and Fabien Laprieur conduct a systematic comparison of parallel components in the BAS and POD frameworks for partitioning compositional dissimilarity into replacement and nestedness-resultant component or into replacement and richness-difference components. In the related blog post, Dr Baselga answers the question ‘What is Beta Diversity?‘

This month’s cover image shows a bumblebee (Bombus sp.) on a flower in Princeton, New Jersey (US). Simulation studies have suggested that to achieve enough statistical power to detect community-wide declines and/or positive responses to agri-environment remedies, large-scale monitoring programmes for bees will require identifying at least hundreds of thousands of bees to species level. Morphology-based taxonomy is infeasible at this scale, and amplicon-based methods (‘metabarcoding’) are prone to false positives and negatives, as well as being unable to provide estimates of species biomass or counts.

In the related article, ‘High-throughput monitoring of wild bee diversity and abundance via mitogenomics‘, Tang et al. apply metagenomic methods to the assessment of bee biodiversity. It is now feasible to assemble hundreds of mitochondrial genomes from insect species, allowing the efficient creation of comprehensive reference databases. As a result, mass bee samples can be shotgun sequenced on high-throughput Illumina sequencers, and the resulting reads mapped to reference mitogenomes. Tang et al.’s pilot study shows that species detection is highly reliable, even for morphologically cryptic species. Moreover, read frequencies are correlated with estimated bee species biomasses, allowing estimates of species counts via a combination of occupancy across traps and estimated biomasses within traps. Mitogenomic methods for biodiversity assessment can be straightforwardly scaled up to hundreds of taxa or more per sample (e.g. ‘all pollinating insects + parasites’) by building up reference databases and increasing sequencing depth.

This article has also received some media attention following a press release. You may have seen it reported in a number of media outlets, including Yahoo! News, the Irish Independent, Phys.org and many more

Photo © Xin Zhou

To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be included in forthcoming issues.

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.

The study of ecological networks helps to understand the biodiversity of our environment and to predict possible extinctions.  Bipartite networks are a special type of ecological network where individuals of a certain species interact with individuals of different species. Bipartite networks are ubiquitous in community ecology, such as the relation between phages (viruses that infect bacteria) and their bacterial hosts.

As Valverde comments “complex networks show common patterns, like nestedness and modularity, and their ecological and evolutionary effects can be studied using theoretical and computational methods”.

A number of tools have been developed to analyze bipartite networks, but BiMat includes new features available for the first time in a single package. Apart from enabling the identification of the key patterns and the evaluation of their statistical significance, this new tool is also capable of performing the multi-scale and meta-analysis of the structure of multiple networks. Furthermore, BiMat includes several visualization tools to explore bipartite networks in either matrix or graph layouts.

Although BiMat was inspired by real problems in microbiology context, is applicable generally for the analysis of systems represented by bipartite networks.  Prominent examples of bipartite networks include mutualistic networks (e.g., plant-pollinator interactions) and antagonistic networks (e.g., virus-plant infection networks).

BiMat has been developed in an object-oriented environment for both MATLAB and Octave platforms. This design enables easy access to all methods and allows for future extensions by the research community. In addition, the companion website provides strong help and a free tutorial.

Media Contacts
Carolina Pozo (UPF Media Room)
Email: carolina.pozo [at] upf.edu

Innovative measuring device enables the water content of biological soil crusts to be measured for the first time.

Biological soil crusts comprising lichens, algae and mosses play an important role in the earth’s ecosystems. They fix carbon dioxide and nitrogen while giving off significant amounts of the greenhouse gas nitrous oxide. Information on soil moisture is of vital importance to investigate their fixation and release processes and to understand them in detail. Previously, no sensor existed that could measure the water content in the top millimeters of the soil with sufficient accuracy. This gap has now been closed by a new development of Bettina Weber and her colleagues at the Max Planck Institute for Chemistry in Mainz, as can be read online in the ‘Early View’ section of the Methods in Ecology and Evolution Wiley Online Library. They have managed to construct an appropriate soil moisture sensor, which delivers reliable data, as well as being cost-effective and flexible to use.

The site, where the soil moisture sensors are installed as a compound of climate stations, is protected from grazing animals by means of a fence. ©Bettina Weber

Biological soil crusts consist of a community of cyanobacteria, lichens, algae and bryophytes, together with fungi, bacteria, and archaea, which grow in the upper three to five millimeters of the soil, forming a hardened layer. They exist in dry regions throughout the world and occupy approximately 20 million square meters, which is almost as large as the surface of South America. All the organisms in biological soil crusts are poikilohydric, which means that they are only active when the soil is sufficiently moist, but survive in an inactive state under dry conditions.

Up to now, the available methods were only moderately suited to at least approximately determine the water content within the top soil level. “The only sensor that can be used in the uppermost layer merely measures whether the organisms are active, but not the water content. All other soil moisture sensors measure the water content in deeper layers, making them totally unsuited for applications in biological soil crusts,” Bettina Weber, group leader in the Multiphase Chemistry Department, describes the problem.

Because the soil moisture in the top five millimeters is essential for the activity, productivity and surface transfer rate of periodically wet organisms, however, Bettina Weber tried to determine this unknown factor by means of an own new development. Together with her research team, she found a method that enabled her to determine the soil moisture by means of its conductivity. The key component of the measuring device is thus a conductivity sensor.

The newly developed soil moisture sensor being used in a lichen-dominated soilcrust in the Succulent Karoo, a semi-desert in South Africa. ©Bettina Weber

The calibration of the sensors posed the biggest challenge: Because the conductivity of the soil is affected not only by its moisture, but also by factors such as its granularity and salt content, the sensors must always be calibrated within the substrate that is being measured. It was only after numerous attempts that the researchers were able to develop a reliable method that enabled them to assign the conductivity values to the corresponding water content values. “As it is really time-consuming to create calibration curves in the laboratory after the field measurements, we have also developed a method to establish a calibration curve that is slightly less accurate but requires fewer field measurements,” states Thomas Berkemeier, doctoral student in the Multiphase Chemistry Department, who developed the mathematical approach for calculating the calibration curves.

As a whole, the new development of the Mainz scientists convinces due to its numerous advantages: Firstly, thanks to its simple structure and robust construction, the sensor can be deployed universally in all kinds of soils around the world. Secondly, the low acquisition costs make it possible to install multiple sensors simultaneously, allowing small-scale patterns and dependencies to be registered in a statistically reliable manner, something that wasn’t possible previously. With simple adjustments, the newly developed soil moisture sensors can be used for measurements over larger soil areas. This makes them potentially useful not only for research projects on biological soil crusts, but also for industrial applications, for instance in the processing of concrete.

The Max Planck scientists have obtained protection for their invention and have registered the moisture sensor as a utility patent. Currently, Bettina Weber is already working on a further development of the sensor, to make it ready for utilization in distributed sensor networks.

Contact:
Dr. Bettina Weber
Email: b.weber [at] mpic.de

Today is 10th National Wildlife Day. As we have done for a few awareness days this year (Bats, Biodiversity and Bees so far) we are marking the day by highlighting some of our favourite Methods in Ecology and Evolution articles on the subject. Obviously ‘wildlife’ is a pretty big topic, so we have narrowed our focus (slightly) to monitoring wildlife (with one or two additional papers that we didn’t want to leave out).

This list is certainly not exhaustive and there are many more wonderful articles on these topics in the journal. You can see more of them on the Wiley Online Library.

If you would like to learn more about National Wildlife Day, you may wish to visit the organisation’s website, follow them on Twitter and Facebook or check out today’s hashtag: #NationalWildlifeDay.

Without further ado though, please enjoy our selection of Methods articles for National Wildlife Day:

Integrating Demographic Data

Our National Wildlife Day celebration begins with an article from our EURING Special Feature. Robert Robinson et al. present an approach which allows important demographic parameters to be identified, even if they are not measured directly, in ‘Integrating demographic data: towards a framework for monitoring wildlife populations at large spatial scales‘. Using their approach they were able to retrieve known demographic signals both within and across species and identify the demographic causes of population decline in Song Thrush and Lawping.

Population Monitoring

Our second article comes from the June 2015 issue of the journal. In this Application article (which is freely available to all), Martha Ellis and her colleagues present rSPACE: an open-source R package for implementing a spatially based power analysis for designing monitoring programs. rSPACE parameterizes a spatially explicit population simulation by incorporating information on species biology and habitat. The authors demonstrate their method and software with an analysis of Wolverine monitoring.

Acoustic Monitoring

The oldest paper that we are highlighting today comes from the December 2012 issue of the journal. As it is over two years old, this paper is also freely available. In ‘Do you hear what I hear? Implications of detector selection for acoustic monitoring of bats‘ Amanda Adams et al. compare the detection of echolocation calls among five commonly used bat detectors. They conclude that it is important to take the choice of detector into account in designing studies and considering bat activity levels among studies using different detectors.

Field Surveys Vs Remote Sensing

Next up is the most recent article that we are highlighting today. In the July 2015 issue of the journal we published Christopher Rhodes et al.’s article ‘The relative value of field survey and remote sensing for biodiversity assessment‘. In this paper, the authors compare high-resolution sample-based field survey (Countryside Survey) with medium-resolution remotely sensed habitat data (a high resolution of Land Cover Map). They conclude that for the best results remote sensing and field survey data should be combined (as did Nathalie Pettorelli in her blog post and her Methods 5th Anniversary talk).

Measuring Diversity

Novel algorithms have been recently developed to estimate alpha and partition beta diversity in all their dimensions. In an Applications article (so, again, freely available to everyone), Pedro Cardoso et al. introduce the R Package BAT (Biodiversity Assessment Tools). This package performs a number of analyses based on either species identities or trees depicting species relationships. The authors include several examples to demonstrate the utility of their method.

Camera Monitoring

In our penultimate National Wildlife Day article, ‘A high-resolution panorama camera system for monitoring colony-wide seabird nesting behaviour‘, Tim Lynch et al. describe the application of a robotic camera system. This system, Gigapan, provides the spatial advantages of aerial photos with the detail and temporal replication of land-based camera systems. It can an extend or enhance traditional data collection methods, particularly for simultaneous observations at distance, of the behaviour of surface nesting colonial seabirds.

Inferring Extinction

As one of the main goals of National Wildlife Day is to protect species that are endangered, we decided to end our celebration of the day with Tamsin Lee’s article ‘A simple numerical tool to infer whether a species is extinct‘. Including uncertain sightings when inferring extinction of a species is relatively new and has proven to be significant, but can lead to mathematical problems. Using a Bayesian model which includes uncertainty around the prior, uncertain sightings and survey effort, the author is able to infer extinction from a sighting record.

We hope that you have a great National Wildlife Day!

Sean is an Associate Editor for Methods in Ecology and Evolution and is a staff scientist at the Smithsonian Institution based at the Smithsonian Environmental Research Center.  His research focuses on the ecological mechanisms that structure forest communities, with interests spanning the fields of demography, physiology, and remote sensing.

The 100th anniversary of the Ecological Society of America was celebrated in Baltimore, Maryland at their Annual Conference in August. This year a record 10,000 ecologists attended the six day event. ESA conferences now boast a staggering number of scientific presentations, ranging from numerous plenary talks, organized oral sessions and regular oral presentation sessions to lightening talks, posters, workshops and mixers. It was both exhilarating and overwhelming, but featured a truly impressive amount of science.

As the sheer magnitude of the event made attending even a fraction of the talks impossible, it feels odd to highlight any particular presentations. Two talks, however – both on the final morning of the conference – did strike me as worth mentioning; not because they featured groundbreaking science, or novel insights, but because they reflect potentially powerful new platforms from which groundbreaking science might develop.

Organizing the herbarium of the new world

Brian Enquist of the University of Arizona, Tuscon opened the Friday organized oral session on “The macroecology of botanical diversity: History, new insights and the central informatics barriers” with an introduction to the Botanical Information and Ecology Network (BIEN), a workflow to standardize and integrate global plant collections and databases.

After thanking the organizers for the coveted Friday 8am slot, Brian demonstrated how the workflow, built by over 50 researchers, collects records of specimens and locations, traits, and genetic code, to build species range maps for approximately 100,000 species across the Americas. Members of BIEN have also created a standardized species list and multi-gene phylogeny for all New World species as well as continental-scale taxonomic, phylogenetic, diversity, and trait maps.

New products from BIEN are detailed diversity maps created using high performance computing through iPlant. These maps have been combined with phylogenetic information and reveal novel patterns of new world diversity. Further, these maps form the basis of a new app, called Plant-O-Matic (available in the iTunes store and elsewhere). This app, recently highlighted in Nature Plants, delivers to the user a list of all plants that are likely to be found in a 100km radius. This should not only offer the public a way to learn about plant distributions and relationships, but also encourage citizen scientists to contribute to the growing BIEN database.

Earth systems models for ecologist who refuse to learn Fortran

The final talk of the organized oral session “Creative Approaches for Addressing Ecological Uncertainty in Earth System Models” was given by Mike Dietze of Boston University (who appropriately finished his talk by declaring the 100th anniversary annual conference officially closed!). Mike presented The Predictive Ecosystem Analyzer (PEcAn), a toolbox for model-data ecoinformatics. He explained how PEcAn’s simple web-based interfaces are designed to bridge the gap between earth systems model developers and the potential users who are not necessarily playfully coding away in Fortran.

A workflow of PEcAn, where experiments and observational studies can improve the uncertainty in predictive models of vegetation dynamics. © Michael Dietze

In fact, Mike sees PEcAn as a way to expand the range of scientists who use earth systems models. The user-friendly toolbox can help anyone who is collecting data that they think could, or should, inform earth system and ecosystem models to play an active role in the comparison between models and data. Experts in sub-disciplines and sub-regions can check how the community of models are doing for the processes and the places that they study. Mike envisions a future where scientists from many disciplines who might conclude a paper or proposal with some variant of “these results should inform models” are able to take the lead in actively implementing this promise.

PEcAn has an expanding menu of Earth Systems Models that it supports, each of which uses distinct approaches to answering similar questions about how climate, the physical world, and the world’s vegetation interact. Users can efficiently design model runs that project vegetation forward under different scenarios or evaluate alternative hypotheses about how ecosystems function. Mike also envisions analyses designed to characterize model uncertainties as playing a role in helping to focus data syntheses and new field observations and experiments on processes with the greatest uncertainty.

These two platforms, and others like them, are laying the groundwork for future breakthroughs in ecological studies. It is exciting to begin to learn about them and about their capabilities. Hopefully, both of these will make significant contributions in the coming years and I wish Mike, Brian and everyone connected with Plant-o-Matic, iPlant and PEcAn the best of luck.

@ Colin (click image to see original)

In recent years, this question has only gotten harder. As more and more journals enter the market, the decision of where to send your paper is becoming increasingly confusing. With predatory journals muddying the waters and an increasing pressure to publish, deciding where to submit can be a daunting task for even seasoned academics.

Is Methods in Ecology and Evolution the right journal for your manuscript? Is your manuscript right for Methods? Hopefully this blog post will give you a set of tools to make that decision a little easier. Most of these can be applied to other journals too (although some may need to be tweaked a little).

Is your paper the kind of thing that Methods is looking for?

Here at Methods we receive many more papers than we are able to publish. Unfortunately, this means that we often have to reject perfectly good manuscripts. One of the most common reasons for a good manuscript to be rejected is that it does not fit within the scope of the journal. Before submitting, it is important to look beyond the journal’s metrics and make sure that your paper is the kind of submission that the Editors are looking for.

Focus: What is the main focus of your article? What do you want readers to take away from it? Hopefully it goes without saying that as a methodological journal, we look for papers with a focus on methods. If your article is more about the results than the methods you used, you may want to consider another journal (For example, we suggest one of great journals in the BES family: Functional Ecology, the Journal of Animal Ecology, the Journal of Applied Ecology or the Journal of Ecology. Not that we’re biased or anything).

Audience: Will your article be interesting to a broad audience? As a generalist journal, we need to consider whether or not a paper is likely to appeal to a large cross-section of our audience. Before submitting, you may want to consider whether your method is:

• Adaptable: Could it be used in a range of systems or applied to a number of organisms/situations? Ask yourself if your paper will be of interest to people who don’t particularly care about your system or chosen organism. If your honest answer is yes, then we would love to consider your paper. If not, you may wish to look for a more specialist journal
• Understandable: Will people outside of your specific field be able to understand your method as you have described it? It is often a good idea to have a colleague in a slightly different field read over your manuscript before submitting. This should, amongst other things, give you a good idea of which terms to spend time explaining and which you can assume the reader understands.
• Novel: Are you describing a new method or an incremental improvement to an existing method? While we would not want to dismiss submissions on improvements out of hand, we tend to look for papers that describe new or significantly changed methods.

Clarity: Have you clearly demonstrated the advantages of your method? As our scope and readership is wide – including statistical methods, phylogenetic analysis, laboratory techniques, field methodology, the development of methods for conservation and more – we aim to publish articles that can clearly be seen as an improvement on previous methods or conventions. If you have not clearly stated what the advantages of your method are, you should add this into your paper before submitting.

Example(s): Do you have a worked example of your method? Whether you have used real-world or simulated data, there should be an example to demonstrate your method somewhere in your manuscript.

As a general journal catering to a diverse community, we are able to consider papers on a wide range of topics. However, it is still important to make sure that the content of your article fits our aims, scope and interests. There are a few ways that you can check this:

• Firstly, read our Aims & Scope and Author Guidelines: these will give you a better idea of what types of articles we are looking for.
• Secondly, look at recent issues and Early View articles to see what has been published. These articles have all been accepted after going through our peer review process, so if you find some that are similar to yours, it’s likely that your manuscript will fit our aims and scope. We have a number of Open Access articles and all of our Applications article are free, so there should always been a good choice of full papers that you can read (and, of course, you can access all of our abstracts).
• Another option is to look at our Associate Editor Board and our Executive Editors. The people on the board will be evaluating your work and (potentially) choosing reviewers for it. If your paper is likely to fit into their areas of expertise, there’s a good chance that it will fit into the journal’s as well.

Is Methods the Best Journal for your Manuscript?

It is equally important to make sure that the journal you are submitting to is right for your article. This could be influenced by requirements of your funder, the structure of your paper, your budget and many other factors. Here are a few factors that you may wish to consider.

Reach: How large of an audience does your article need to have? Do you want it to be read globally or will it mainly be of interest in a specific region? Methods has a large international readership. Publishing with us is an excellent way to explain your method to a broad and diverse audience. Our articles are freely accessible in many developing countries and become free to everyone two years after issue publication. If you want people studying different topics around the world to see your work, Methods is definitely a journal to consider. For articles with a narrow geographic focus that are unlikely to be of interest to people outside of a certain area, regional journals may be a better choice. Similarly, for articles that are likely to appeal to only a small research community, it may be best to consider a specialist journal.

Fees: If you have been working on your paper for a long time, your budget may be running low. While many journals charge page fees, it is completely free to publish with Methods. As we are an online only publication, we don’t even have colour charges for your figures!

Open Access: Many funders require you to make your article Open Access upon publication. Methods is a hybrid journal and we can accommodate Open Access papers (through Wiley’s OnlineOpen option). If you are a member of the British Ecological Society (BES), you can get a discount on the OA charges as well. We do not ask whether your paper will be Open Access until after it has been accepted, so if you are unsure when you submit, that’s not a problem.

Data Archiving: As a BES journal, we are proud to actively support data archiving. As well as requiring that data supporting any paper is appropriately archived (in a freely available repository which guarantees the permanence of the data), we also sponsor deposits in Dryad. If you are unable or unwilling to archive your data, we may not be able to publish your paper (but we will always consider the circumstances before making a final decision).

Visibility: As mentioned above, one of the consequences of the proliferation of new journals is that it is difficult to decide where to publish. It also means that it can be difficult to make sure that your article is found by the people who you want to read it. One of the ways that journals make sure that people can find your paper is through indexing services. You can see where Methods is indexed here. In addition to this, we have a large social media following (on Twitter, Facebook, Google+, YouTube and here on the blog). We use these avenues to highlight new and key articles, making sure that as many people as possible see our authors’ work.

Online Extras: For many methodological articles it is helpful to have a tutorial video or a blog post explaining how and why the method can be used in a less formal manner. We are able to offer a number of options for extra information online and we are more than happy to discuss and consider any ideas that you may have for your paper. If you would like to provide readers with a little more information alongside your article, we are very well placed to help out.

Hopefully this post will make your decision on whether or not to submit your article to Methods in Ecology and Evolution a little easier. As mentioned above, you can find more information on our website. The Author Guidelines and Aims & Scope pages are great places to start. You can get more information on the journal from the Editorial that was included in our first issue too.

If you would like some more general advice on how to select a journal for your paper, you may wish to watch this presentation by Roohi Ghosh on BrightTALK. BrightTALK is free, but you need to sign up to access the content.

If you are still unsure about whether to submit to Methods, you can always email the Editorial Office to ask for advice.

Tim is an Associate Editor who works on Applications submissions for Methods in Ecology and Evolution. His research interests include spatial and temporal dynamics of species interactions at the community level, the relevance of variability in community structure on emerging ecosystem properties, and the evolutionary dynamics of multi-species assemblages.

I am back from the centennial meeting of the Ecological Society of America. I met a lot of great people, saw a lot of great talks, and had lovely discussions. One thing that has been in the back of my mind for a while though, is the question of how much methodology should go into an oral presentation?

How much methodology should be in your presentation? © Phil Whitehouse

Methods are important  —  over the last two years I have found that this has been the part of papers I criticize the most during peer review. Any result is only as robust as its least robust element and there are, in ecology, enough sources of variability that we do not want methods to add any more. As a consequence, appreciating a result and its robustness require that we be able to understand and evaluate the methods by which this result has been obtained.

There are a few elements to evaluating a method. Does it rely on a sound and tested theory? Is it properly applied? Is the method correctly implemented? All of these questions (and some more) should be asked —  and answered in the affirmative  —  before we decide to accept a result. If not, we are putting ourselves in the position to blindly accept what we are being told.

Let me illustrate. Imagine that I say, or write, “I modelled the growth of this population using a Leslie matrix to estimate the age distribution”. What I am really meaning is “I have a population of interest. I have correctly determined biologically meaningful age classes. I have a correct estimate of the number of individuals in each class. I know, or can estimate, the rate of transition between these classes, and their fecundity. I assume that these rates are not dependent upon other parameters. I assume that linear algebra, which I used to estimate the distribution of ages, is correct.” Each one of these clauses has to be evaluated in the same way because the correct result (the distribution of ages in my population) can only be reached if all of these clauses are correct.

Of course, some of the underpinnings of methods we use are widely accepted. There is no need to re-explain linear algebra, calculus, or basic probabilities. Nonetheless, this leaves open the questions of “Is the method appropriate?” (which gives insurance that the appropriate thing has been done), “Has the method been applied correctly?” (which gives insurance that the appropriate thing has been done well), and “How does it work?” (which gives an indication of the possible biases).

For an example of why this actually matters, look no further than Christie Aschwanden’s entry in FiveThirtyEight: given the same data, to ask the same question, it is not at all uncommon that different researchers will use different methods, and therefore reach different conclusions. Any evaluation of the quality of a result requires the evaluation of the quality of the method.

This brings me back to the question of how much time should we spend on describing methods during an oral presentation? The average presentation, leaving time for discussion, and for people to change rooms, is probably barely above 15 minutes. This is not much time to introduce the general context, build a narrative, and walk people through the implication of the results. Let alone go into all of the details of the methods that have been used.

In fact, my own presentation uses a method that I present in two slides. The original presentation of this method (in PDF) took 42 slides and one paper with copious appendices! Had I wanted to give a full explanation of how it works, I would have run out of time, and used the time slots of the two speakers that came after me.

Spending more time on the method can be boring for the audience (and there might be equations). Not spending any time at all (I’ve seen this) is effectively hand-waving. Spending a moderate amount of time (I’ve done this) is difficult. Saying which method was used is rarely very informative. It is better than nothing, probably, but it is not great.

As an audience member, this places me in a very uncomfortable position. On one hand, I really want to trust all of this new, intriguing, exciting science. On the other hand, I am not prepared to suspend my disbelief long enough to forget about the fact that the result is meaningless unless framed within the context of the methods used to reach it. And a conference talk is a very poor way to do the later — even posters are better at it!

So what should we do? Many fields publish papers as part of the conference proceedings; this is one possible way. Unfortunately the tradition in life sciences is that conference proceedings have very little value.

Using something to supplement the talk itself would be good though. Do we have something like this? Yes! We have preprints. Preliminary versions of a manuscript that are nearly good enough to be submitted (or in fact, are under review already), that anyone can read.

So here is my proposal: give a big boost to talks that are accompanied by a preprint (or even a published paper). Highlight them in the program in some way, or require them for organized sessions. If we spend so much money on attending conferences, it is because we consider them an important part of the scientific activity. It would therefore make sense that their content is held to the same rigorous standards of quality and scrutiny than the rest of our scientific production.

Talking is well and good, but show us some text.

© Tim Poisot

Before publishing your manuscript in a preprint repository, it is a good idea to check the preprint policy of journals that you intend to submit to. Methods in Ecology and Evolution is happy to consider articles that have been published in preprint repositories or on authors’ personal websites. See here for more details.

Animal proteins only make up a small part of a black bear’s diet. ©PLF73 (Click image to see original)

Black bears in Yosemite National Park that don’t seek out human foods subsist primarily on plants and nuts, according to a study conducted by biologists at UC San Diego who also found that ants and other sources of animal protein, such as mule deer, make up only a small fraction of the bears’ annual diet.

Their study, published in Methods in Ecology and Evolution, might surprise bear ecologists and conservationists who had long assumed that black bears in the Sierra Nevada rely on lots of protein from ants and other insects because their remains are frequently found in bear feces. Instead, the researchers believe that bears likely eat ants for nutrient balance.

Rather than relying on indigestible foods found in bear feces, the UC San Diego ecologists looked at the digestible foods that were used to produce bear tissue. They accomplished this by measuring the abundances of carbon and nitrogen isotopes found in different species of plants and animals, and used a statistical approach to relate them to the carbon and nitrogen isotopes measured in bear hair. This allowed the scientists to quantify what the bears ate, then assimilated into their hair.

The scientists also applied the same technique to Norway rats in Alaska’s Aleutian Islands and determined that this invasive species subsisted largely on terrestrial plants and seasonal pulses of marine amphipods, rather than marine birds as had been long assumed.

“Rats tend to dominate the habitats they invade on islands, killing much of the native fauna, especially birds, which is a serious conservation issue,” said Carolyn Kurle, an assistant professor of biology at UC San Diego who conducted the study with Jack Hopkins, a postdoctoral fellow. “Using stable isotopes, we confirmed that marine birds have been extirpated to such levels on the islands where we worked that rats don’t eat them anymore.”

“Both rats and black bears are omnivores with complex diets consisting of both plants and animals,” said Hopkins. “To our knowledge, no study before this has accurately estimated the relative importance of plants and animals to the diets of these omnivore populations.”

Acorns are an important part of a black bear’s diet. ©Edd Prince (click image to see original)

Hopkins said he and Kurle found in their study that plants and acorns are black bears’ primary food sources in Yosemite. “We also learned that female bears foraged for high-fat acorns and pine nuts more heavily than males, suggesting that females likely need these seeds for reproduction. This could be a real problem for Sierra black bears in the future if blister rust continues to kill sugar pines and sudden oak death moves in from the coast.”

Besides resolving the issue of what black bears and Norway rats actually use for growth and function, the scientists said a major goal of their study was to demonstrate how the use of stable isotopes derived from animal tissues and their prey could be used to quantify the resource use of other omnivores with complex diets.

“Ecologists currently focus too much attention on measuring the variation of isotope data for consumers and their prey and not enough attention on quantifying the interactions of consumers and their prey using isotope data,” Hopkins explained. “Measuring such interactions and their relative strengths can help us understand the impacts animals have on their environment.”

Over the past two decades, black bears in Yosemite were involved in more than 12,000 reported incidents within the national park, injuring nearly 50 people and causing $3.7 million worth of property damage. In response to these problems, Congress has appropriated over $8 million since 1999 to mitigate human-bear conflicts in Yosemite.

Those efforts appear to be working. In a study published last year in the journal Frontiers in Ecology and the Environment, Hopkins and other scientists measured the stable isotopes of carbon and nitrogen in the hair and bone of Yosemite bears over the past century and found that since 1999, the proportion of human-derived food in bear diets has dramatically declined.

“Yosemite bears currently consume human foods in a similar proportion as they did in the early 1900s,” said Hopkins. “This suggests a notable management achievement in the park, considering that thousands of people visited Yosemite annually in the early 1900s, while about four million people visit each year today.”

The UC San Diego study was funded by grants from the U.S. Fish and Wildlife Service, National Science Foundation, Environmental Protection Agency, Center for the Dynamics and Evolution of the Land-Sea Interface, STEPS Institute for Innovation in Environmental Research, UC San Diego and the Yosemite National Park Bear Council.

Media Contacts
Kim McDonald (UC San Diego Communications and Public Affairs)
Email: kmcdonald [at] ucsd.edu

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.

Bee Soup

©Umberto Salvagnin

Last month, we published ‘High-throughput monitoring of wild bee diversity and abundance via mitogenomics‘ by Tang et al. in Early View. In this article, the authors proposed a new method  to monitor the wild bee populations using, as the title mentions, mitogenomics. This allows for quick and accurate identification of bee species and can help conservationists to see where species are declining and where their efforts are working. This somewhat counter-intuitive method has also received some media attention and was featured in a number of news outlets. This article is Open Access.

Pollinator Networks

Next we have an Applications article, which means that this paper is free to access for anyone (and has been since it was first published!). In ‘A method for detecting modules in quantitative bipartite networks‘ Dormann and Strauss introduce an algorithm to identify modules in quantitative bipartite (or two-mode) networks. It is a significant improvement on previous standards of algorithms for binary networks and allows for the detection of modules in the typically noisy data of ecological networks.

Lethal Sampling

In another recent article, Gezon et al. describe an experiment in which they assessed whether lethal sampling for bees using pan traps and netting affected bee abundance and diversity when done often and over an extended time period. ‘The effect of repeated, lethal sampling on wild bee abundance and diversity‘ shows that the standardized method for sampling bees did not affect bee communities in terms of abundance, rarefied richness, evenness, or functional group composition.

Flower Visitation and Pollination

King et al. demonstrate a practical measure of pollinator effectiveness in ‘Why flower visitation is a poor proxy for pollination: measuring single-visit pollen deposition, with implications for pollination networks and conservation‘. Their method helps to distinguish between ‘pollinators’ and ‘visitors’ – a crucial differentiation in pollinator networks – and reveals how effective specific pollinators can be. It could help to avoid potential misinterpretations of the conservation values of flower visitors and of possible extinction threats.

Bee Vision

Lesser Celandine in human-vision (left) and honey bee vision (right). There’s a striking colour difference in UV. The whole flower looks yellow to us, however the petals reflect UV strongly and absorb blue, while the pollen in the centre doesn’t reflect UV, so looks red. This makes the flower look much more colourful to bees than ourselves.

Have you ever wondered how honey bees and other pollinators see the world? Well now you can find out! In ‘Image calibration and analysis toolbox – a free software suite for objectively measuring reflectance, colour and pattern‘ Troscianko and Stevens introduce software that converts photographs to ‘animal vision’. This software can show how pollinators, such as bees, that can see in ultra-violet. The researchers behind the software have provided specific data on camera settings for honey bees as well as a number of other commonly studied species. This is another article that has received considerable press attention (including articles in The Independent, The New York Times, The Washington Post and more). This article is Open Access.

For more articles on honey bees and other pollinators, check out our Pollinator Ecology Virtual Issue, published in January 2014. It includes articles from all five BES journals (Functional Ecology, the Journal of Animal Ecology, the Journal of Applied Ecology, the Journal of Ecology and, of course, Methods in Ecology and Evolution).

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.

We also see the issue publication of one of the articles from our Virtual Issue on ‘Advances in Phylogenetic Methods‘ this month. Douglas Chesters et al. demonstrate an implementation for multigene DNA barcoding in ‘A DNA Barcoding system integrating multigene sequence data‘. Their approach adds to the established species-dense DNA barcode backbone with other genomic data, reducing error via integration of independent genetic loci and permitting additional identifications for non-barcode fragments.

The cover image shows two climbers ascending a 91 metre Douglas-fir (Pseudotsuga menziesii) in western Oregon, USA. The subject tree in the photograph is adjacent to the world’s tallest Douglas-fir which was climbed via ropes and measured to be 99.6 metres in height. Due to the scale in size, height and breadth of tree crowns, rope-based access is often required to accurately measure the dimensions of the tree and is likewise used for ecological studies on pollination; gas exchange; tree growth; fruit dispersal; diversity of epiphytes, invertebrates, and vertebrates; the atmosphere/biosphere interface; herbivory; ecosystem services; and climate change.

Rope-based canopy access is the key to unlocking the ecology of the upper reaches of the forest because it is relatively inexpensive and provides replicated sampling of canopy organisms, structures and spaces. It can also be dangerous, especially when methods and equipment not specified for tree climbing are used. To improve safety and aid climbers, David Anderson et al. set out to create a user’s guide to 40 years of published literature on canopy access methods. In ‘Review of rope-based access methods for forest canopy’ they critique written descriptions of safe and unsafe climbing practices and list the climbing methods contained in every source.

Photo © Paul Colangelo
To see more of Paul Colangelo’s wonderful photography, please visit his Website and follow him on Twitter and Facebook.

To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be included in forthcoming issues.