Fourier Methods Gain Wide Appeal for Tropical Phenology Analysis

Post provided by Emma Bush

Lopé National Park. ©Jeremy Cusack

Lopé National Park. ©Jeremy Cusack

Like all living things, plant species must reproduce to persist. Key stages in successful plant reproduction must be carefully timed to make sure resources are available and conditions are optimal. There will be little success if flowers mature in bad weather conditions for their insect pollinators or if fruits ripen but the seed dispersers have migrated elsewhere.

Because plants rely on the abiotic environment for sunlight, nutrients and water, and in some cases for the dispersal of pollen and seeds, it is not surprising that their life stages are closely linked to environmental cycles. Continue reading

The Global Pollen Project: An Update for Methods Readers

Post Provided by Andrew C. Martin

The Global Pollen Project is an online, freely available tool and data source developed to help people identify and disseminate palynological resources. Palynology – the study of pollen grains and other spores – is used across many fields of study including modern and fossil vegetation dynamics, forensic sciences, pollination, and beekeeping. To help make pollen identification quicker and more transparent, we developed the Global Pollen Project (GPP) – an open, peer-reviewed database of global pollen morphology, where content and expertise is crowdsourced from across the world. Our approach to developing this tool was open: open code, open data, open access. It connects to other data services, including the Global Biodiversity Information Facility and Neotoma Palaeoecology Database, to provide occurrence data for each taxon, alongside pollen images and metadata. Continue reading

How Strong is Natural Selection? Stitching Together Linear and Nonlinear Selection on a Single Scale

Post provided by Robert May Prize Winner Jonathan Henshaw

Some individuals survive and reproduce better than others. Traits that help them do so may be passed on to the next generation, leading to evolutionary change. Because of this, evolutionary biologists are interested in what differentiates the winners from the losers – how do their traits differ, and by how much? These differences are known as natural selection.

Linear and Nonlinear Selection

Traditionally, natural selection is separated into linear selection (differences in average trait values) and nonlinear selection (any other differences in trait distributions between winners and the rest). For example, successful individuals might be unusually close to average: this is known as stabilizing selection. Alternatively, winners might split into two camps, some with unusually high trait values, and others with unusually low trait values. This is disruptive selection (famously thought to explain the ur-origin of sperm and eggs). Stabilizing and disruptive selection are important types of nonlinear selection. In general, though, the trait distribution of successful individuals can differ from the general population in arbitrarily complicated ways.

When individuals with larger trait values have higher fitness on average (left panel), the trait distribution of successful individuals is shifted towards the right (right panel, orange curve). The difference in mean trait values between the winners and the general population is called linear selection.

When individuals with larger trait values have higher fitness on average (left panel), the trait distribution of successful individuals is shifted towards the right (right panel, orange curve). The difference in mean trait values between the winners and the general population is called linear selection.

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2017 Robert May Prize Winner: Jonathan Henshaw

The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2017 winner is Jonathan Henshaw, for his article ‘A unified measure of linear and nonlinear selection on quantitative traits.

The standard approach to quantifying natural selection, developed by Lande and Arnold, does not allow for comparable metrics between linear (i.e. selection on the mean phenotype) and nonlinear (i.e. selection on all other aspects of the phenotypic distribution, including variance and the number of modes) selection gradients. Jonathan Henshaw’s winning submission provides the first integrated measure of the strength of selection that applies across qualitatively different selection regimes (e.g. directional, stabilizing or disruptive selection). Continue reading

HistMapR: 12 Months from Coffee Break Musings to a Debut R Package

Post provided by Alistair Auffret

I was really happy to hear that our paper, ‘HistMapR: Rapid digitization of historical land‐use maps in R’ was shortlisted for the 2017 Robert May Prize, and to be asked to write a blog to mark the occasion. The paper was already recommended in an earlier blog post by Sarah Goslee (the Associate Editor who took care of our submission), and described by me in an instructional video, so I thought that I would write the story of our first foray into making an R package, and submitting a paper to a journal that I never thought I would ever get published in.

Background: Changing Land-Use and Digitizing Maps

Land-use change in Europe is often typified by land-drainage to create arable fields.

Land-use change in Europe is often typified by land-drainage to create arable fields.

Land-use change is largely accepted to be one of the major threats to biodiversity worldwide at the moment. At the same time, a warming climate means that species’ ranges need to move poleward – something that can be hampered by changing land use. Quantifying how land use has changed in the past can help us to understand how species diversity and distributions respond to environmental change.

Unfortunately, quantifying this change by digitizing historical maps is a pretty tedious business. It involves a lot of clicking around various landscape features in a desktop GIS program. So, in many cases, historical land use is only analyzed in a relatively small number of selected landscapes for each particular study. In our group at Stockholm University, we thought that it would be useful to digitize maps over much larger areas, making it possible to assess change in all types of landscape and assess biodiversity responses to land-use change at macroecological scales. The question was, how could we do this? Continue reading

Solo: Developing a Cheap and Flexible Bioacoustic Tool for Ecology and Conservation

Post provided by Robin Whytock

A Solo recorder in the field. ©Tom Bradfer-Lawrence

A Solo recorder in the field. ©Tom Bradfer-Lawrence

Ecologists have long been fascinated by animal sounds and in recent decades there’s been growing interest in the field of ‘bioacoustics’. This has partially been driven by the availability of high-definition digital audio recorders that can withstand harsh field conditions, as well as improvements in software technology that can automate sound analysis.

Sound recordings can be used to study many aspects of animal behaviour in a non-intrusive way, from studying the social dynamics of monkeys or even clownfish to detecting echolocating bats or singing birds. Some species can only reliably be separated in the field by the sounds that they make, such as common and soprano pipistrelle bats. Bat research in general has been revolutionised by commercially available acoustic loggers, with some amazing advances using artificial intelligence to automatically detect bat calls. Continue reading

Radar Wind Profilers: A Widespread but Unused Remote Sensing Tool for Migration Ornithologists

Post provided by Nadja Weisshaupt

Snapshot of nocturnal waterfowl migration in front of the lunar disk. ©N. Weisshaupt

Snapshot of nocturnal waterfowl migration in front of the lunar disk. ©N. Weisshaupt

Each year an uncountable number of airborne organisms, mainly birds and insects, venture out on long journeys across the globe. In particular, the mass movements of birds have fascinated humankind for hundreds of years and inspired a wealth of increasingly sophisticated studies. The development and improvement of individual tracking devices in animal research and has provided amazing insights into such extensive journeys. Study of mass movements of biological organisms is still a challenge on continent-wide or cross-continental scales.

One tool that can effectively track and/or monitor large numbers of birds is radar technology. Radars offer many advantages over other methods such as visual counts or ringing. They’re less expensive, need less effort, offer better visibility and detectability, and are more applicable for large-scale monitoring. Networks of meteorological radars (as opposed to individual radars) seem particularly promising for large-scale studies. Continue reading

Meta-Analysis: How to Increase the Reach of Your Research and Make it Longer Lasting

Post provided by Katharina Gerstner

Like each coral, every single primary research study contributes to the larger picture.  © Wise Hok Wai Lum

Like each coral, every single primary research study contributes to the larger picture. © Wise Hok Wai Lum

Quantitative syntheses of primary research studies (meta-analysis) are being used more and more in ecological and evolutionary research. So knowing the basics of how meta-analysis works is important for every researcher. Meta-analytical thinking also encourages us scientists to see each single primary research study as a substantial contribution to a larger picture.

To be included in a meta-analysis, relevant primary research studies must be easy to find and basic information about the methods and results must be thoroughly, clearly and transparently reported. Moreover, papers with accessible data are the most useful for meta-analyses. Many published papers provide this information, but it’s not unusual for essential data to be omitted. Studies that are missing these details can’t be used in meta-analyses, which limits their reach. Continue reading

piecewiseSEM: Exploring Nature’s Complexity through Statistics

Post provided by Jonathan S. Lefcheck

Nature is complicated. As a scientist, you might say, “Well, duh,” but as students of nature, this complexity is probably the single greatest challenge we must face in trying to dissect the hows and whys of the natural world.

History is a Set of Lies Agreed Upon: Moving beyond ANOVA

For a long time, we tried to strip this complexity away by conducting very controlled experiments adhering to rigid designs. The ‘two-way fully-crossed analysis of variance’ will be familiar to anyone who has taken even the most basic stats class, because, for many decades, it was the gold standard for any experiment.

It might be tough to manipulate this whole reef.

The problem is: the real world doesn’t adhere to an ANOVA design. By this, I mean that by their very nature, manipulative experiments are artificial. It’s hard—if not impossible—to manipulate an entire forest or a coral reef, and as such, we retreat to more tractable, smaller investigations. There is certainly a lot of value in determining whether the phenomenon can occur, but these tightly regulated designs say nothing about whether they are likely to occur, particularly at the scales most relevant to humanity.

To get at the latter point, we must leave the safety of the greenhouse. However, our trusty ANOVA toolbox isn’t very useful anymore, because real-world data often violate the most basic statistical assumptions, not to mention the presence of numerous additional influences that may drive spurious relationships. Continue reading

Googling for Ecological Answers: Using the Morphic Web Application

Post provided by Gabriella Leighton

Online Images: A Treasure Trove of Ecological Data

In the proclaimed ‘information age’, where answers are available at the click of a button or a swipe of a finger, we have become accustomed to the ability to get an almost instant grasp of any topic. Other fields are already making use of this wealth of easily accessible online data, but biologists and ecologists tend to let it slip by. However, this attitude is slowly beginning to change. Some ecological and evolutionary studies are emerging that have used the internet to gather data – through online citizen science projects (e.g. Evolution MegaLab) or databases (e.g. using Google Trends) – but few have used existing data, particularly publicly available data from image repositories.

We were curious to apply the concept of using existing images on the internet to a fascinating visual biological phenomenon: colour polymorphism (or the occurrence of multiple discrete colour phenotypes). To do this, we planned to exploit an existing penchant people have for uploading photographs of animals to the Internet.

Our search phrases included the common and scientific name of the species, as well as a location-specific term

Our search phrases included the common and scientific name of the species, as well as a location-specific term

Continue reading