Oxford Research Sheds Light on the Secret Life of Badgers

Below is a press release about the Methods paper ‘An active-radio-frequency-identification system capable of identifying co-locations and social-structure: Validation with a wild free-ranging animal‘ taken from the University of Oxford.

© Peter Trimming

Detecting the movements and interactions of elusive, nocturnal wildlife is a perpetual challenge for wildlife biologists. But, with security tracking technology, more commonly used to protect museum artwork, new Oxford University research has revealed fresh insights into the social behaviour of badgers, with implications for disease transmission.

Previous studies have assumed that badgers are territorial and, at times, anti-social, living in tight-knit and exclusive family groups in dens termed ‘setts’. This led to the perception that badgers actively defend territorial borders and consequently rarely travel beyond their social-group boundaries.

This picture of the badger social system is so widely accepted that some badger culling and vaccination programmes rely on it – considering badger society as being divided up into discrete units, with badgers rarely venturing beyond their exclusive social-groups. But, the findings, newly published in Methods in Ecology and Evolution, have revealed that badgers travel more frequently beyond these notional boundaries than first thought, and appear to at least tolerate their neighbours. Continue reading

Conditional Occupancy Design Explained

Occupancy surveys are widely used in ecology to study wildlife and plant habitat use. To account for imperfect detection probability many researchers use occupancy models. But occupancy probability estimates for rare species tend to be biased because we’re unlikely to observe the animals at all and as a result, the data aren’t very informative.

In their new article – ‘Occupancy surveys with conditional replicates: An alternative sampling design for rare species‘ – Specht et al. developed a new “conditional” occupancy survey design to improve occupancy estimates for rare species, They also compare it to standard and removal occupancy study designs. In this video two of the authors, Hannah Specht and Henry Reich, explain how their new conditional occupancy survey design works. 

This video is based on the article ‘Occupancy surveys with conditional replicates: An alternative sampling design for rare species‘ by Specht et al.

 

Refined DNA Tool Tracks Native and Invasive Fish

Below is a press release about the Methods paper ‘Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA‘ taken from the Cornell University.

©Nick Hobgood

Rather than conduct an aquatic roll call with nets to know which fish reside in a particular body of water, scientists can now use DNA fragments suspended in water to catalog invasive or native species.

The research from Cornell University, the University of Notre Dame and Hawaii Pacific University was published July 14 in Methods in Ecology and Evolution.

“We’ve sharpened the environmental DNA (eDNA) tool, so that if a river or a lake has threatened, endangered or invasive species, we can ascertain genetic detail of the species there,” said senior author David Lodge, the Francis J. DiSalvo Director of the Atkinson Center for a Sustainable Future at Cornell, and professor of ecology and evolutionary biology. “Using eDNA, scientists can better design management options for eradicating invasive species, or saving and restoring endangered species.” Continue reading

Drones used to assess health of Antarctic vegetation

Below is a press release about the Methods paper ‘Unmanned aircraft system advances health mapping of fragile polar vegetation‘ taken from the University of Wollongong.

New method faster, more efficient and less damaging to the environment

A team of researchers from the University of Wollongong (UOW) and the University of Tasmania has developed a new method for assessing the health of fragile Antarctic vegetation using drones, which they say could be used to improve the efficiency of ecological monitoring in other environments as well.

The researchers have written about their method in an article published in Methods in Ecology and Evolution, a scientific journal of the British Ecological Society.

Continue reading

Issue 8.7

Issue 8.7 is now online!

© Paula Matos

The July issue of Methods is now online!

This issue contains three Applications articles (one of which is Open Access) and one additional Open Access article. These four papers are freely available to everyone, no subscription required.

BioEnergeticFoodWebs: An implementation of Yodzis & Innes bio-energetic model, in the high-performance computing language Julia. This package can be used to conduct numerical experiments in a reproducible and standard way.

 Controlled plant crosses: Chambers which allow you to control pollen movement and paternity of offspring using unpollinated isolated plants and microsatellite markers for parents and their putative offspring. This system has per plant costs and efficacy superior to pollen bags used in past studies of wind-pollinated plants.

 The Global Pollen Project: The study of fossil and modern pollen assemblages provides essential information about vegetation dynamics in space and time. In this Open Access Applications article, Martin and Harvey present a new online tool – the Global Pollen Project – which aims to enable people to share and identify pollen grains. Through this, it will create an open, free and accessible reference library for pollen identification. The database currently holds information for over 1500 species, from Europe, the Americas and Asia. As the collection grows, we envision easier pollen identification, and greater use of the database for novel research on pollen morphology and other characteristics, especially when linked to other palaeoecological databases, such as Neotoma.

Continue reading

Getting Serious About Transposable Elements

Post Provided by: Gabriel Rech and José Luis Villanueva-Cañas

So Simple yet so Complex

A long standing research topic in evolutionary biology is the genetic basis of adaptation. In other words, how does a novel trait appear (or spread) in response to an environmental change? Despite the rapid advances in sequencing over the last two decades, we have only been able to fully characterize a few adaptations.

As stated by Richard Dawkins in Climbing Mount Improbable, while natural selection is a very simple process, modeling natural selection and determining its causes, effects and consequences is an extremely difficult task. Also, most of our efforts so far have been focused on just one type of genetic variation: single nucleotide polymorphisms (SNPs). Other types of variations such as transposable element (TE) insertions have received much less attention. Paradoxically, some great examples of the role of TEs in adaptation have been right under our noses the whole time, in basic biology textbooks. Continue reading

Why Soft Sweeps from Standing Genetic Variation are More Likely than You May Think

We coined the term “soft sweeps” in 2005. The term has since become widely used, though not everyone uses the term in the same way. As part of the ‘How to Measure Natural Selection‘ Special Feature in Methods in Ecology and Evolution, we attempt to clarify what “soft sweep” means and doesn’t mean. For example, not every sweep from standing genetic variation is necessarily a soft sweep.
In the review paper we also show under what conditions soft sweeps are likely (e.g., high population-wide mutation rate, multi-locus selection target). Finally, we describe relevant examples in fruitflies, humans and microbes and we discuss future research directions.
The video focuses on one aspect of the paper, which is illustrated in figure 3: “Why soft sweeps from standing genetic variation are more likely than you may think.”

This video is based on the Open Access article ‘Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation by Hermisson and Plennings in the ‘How to Measure Natural Selection‘ Special Feature.

 

Evolutionary Quantitative Genetics: Virtual Issue

Post provided by Michael Morrissey

©Dr. Jane Ogilvie, Rocky Mountain Biological Laboratory

Evolutionary quantitative genetics provides formal theoretical frameworks for quantitatively linking natural selection, genetic variation, and the rate and direction of adaptive evolution. This strong theoretical foundation has been key to guiding empirical work for a long time. For example, rather than generally understanding selection to be merely an association of traits and fitness in some general way, theory tells us that specific quantities, such as the change in mean phenotype within generations (the selection differential; Lush 1937), or the partial regressions of relative fitness on traits (direct selection gradients; Lande 1979, Lande and Arnold 1983) will relate to genetic variation and evolution in specific, informative ways.

These specific examples highlight the importance of the theoretical foundation of evolutionary quantitative genetics for informing the study of natural selection. However, this foundation also supports the study other critical (quantification of genetic variation and evolution) and complimentary (e.g., interpretation when environments, change, the role of plasticity and genetic variation in plasticity) aspects of understanding the nuts and bolts of evolutionary change. Continue reading

Britain’s Smallest Bird Affected by Cold Winters: New Analysis Methods Relate Wildlife Abundance to Weather

Below is a press release about the Methods paper ‘Attributing changes in the distribution of species abundance to weather variables using the example of British breeding birds‘ taken from the University of St Andrews.

©CJ Hughson

The goldcrest is being hit hard by cold winters. ©CJ Hughson

Britain’s smallest bird species, the goldcrest, is being hit hard by cold winters, new analysis methods developed by researchers at the University of St Andrews have revealed.

The data analysis techniques, published today in Methods in Ecology and Evolution, take a longer term view over multiple locations and for a period of several years, compared to previous studies.

They showed that the cold temperatures strongly affected breeding numbers of the goldcrest, while in contrast, the song thrush was not affected by the cold, but benefited from wet and mild summers. Continue reading

BES Guide to Reproducible Code: Tips and Tricks Needed

The British Ecological Society is currently working on a Guide to Reproducible Code. This will follow on from our previous Guides to Peer Review, Data Management and Getting Published. All of our Guides are intended to provide Early Career Researchers with a concise and easy to understand introduction to the topic. You can download them for free on our website.

Each Guide includes short pieces of advice provided by academics who are familiar with the topic – and this is where you come in. We’re looking for tips and tricks to help Early Career Researchers looking to make their code reproducible and we would like your help.

We’ve set up a Google form with sections that relate to the broad areas that will be covered in our Guide to Reproducible Code:

  1. Organising Code
  2. Writing Code
  3. Report Writing
  4. Versioning
  5. Archiving Code
  6. Additional Resources

The guide is intended for people who are fairly new to coding, so please don’t be too technical. There are options to enter three pieces of advice in each section (if you’ve got more tips and tricks, feel free to fill in the form multiple times). We’ll choose the best pieces of advice and publish them in the Guide, along with the name and affiliation of the person who provided them.

You can submit your Tips and Tricks for Making Code Reproducible here. Thank you for contributing to our Guide.