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.

New Associate Editors

Today we are welcoming four new Associate Editors to Methods in Ecology and Evolution. Graziella Iossa (University of Lincoln) and Theoni Photopoulou (Nelson Mandela Metropolitan University) are joining as regular Associate Editors and Simon Jarman (Unversity of Porto) and Daniele Silvestro (University of Gothenburg) will be working on Applications articles. You can find out more about all of our new Associate Editors below.

Graziella Iossa

“I am an evolutionary ecologist with broad interests in behavioural and population ecology. My research has explored reproductive strategies and the evolution of male and female reproductive traits in mammals and insects and I have used a range of techniques to study the behaviour and welfare of wildlife. I have just started to explore interdisciplinary approaches with the aim to improve our understanding of the value and role of ecosystem services in human health, specifically for antimicrobial resistance.”

Graziella’s most recent paper – Micropyle number is associated with elevated female promiscuity in Lepidoptera – investigates the evolution of the micropyle, a tiny canal which sperm use to fertilise eggs in insects. This is the first study to show that micropylar variation is driven by female promiscuity – the more micropyles her eggs have, the more choice she is likely to have over which male fathers her offspring. Also, Graziella currently holds a NERC Valuing Nature placement which aims to combine perspectives from evolutionary ecology, microbial ecology, epidemiology, ecosystem science and public health to develop a new, holistic way of understanding antimicrobial resistance

Simon Jarman

“Methods employing epigenetics, environmental DNA analysis or bioinformatics for ecological research are improving rapidly and have clear potential for future development. My research focuses on creating new methods in these areas and using them to study population biology and biodiversity. Epigenetic markers for physiological features such as biological age can be used to determine key features of population biology such as age class distribution. Environmental DNA can be used to measure species distributions; biodiversity in environmental samples; and animal diet composition. I am interested in the molecular biology and computational approaches that are required to implement these methods; as well as how they can be used to study specific ecological questions.”

In November 2016, Simon published an Open Access article in Methods in Ecology and Evolution. ‘Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates‘ explains how to collect scat samples to optimise the detection of food DNA in vertebrate scat samples. More recently, Simon was the last author of ‘KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)‘ – which introduces the most advanced genetic database on Euphausia superba, KrillDB, and includes comprehensive data sets of former and present transcriptome projects.

Theoni Photopoulou

“I am interested in the way biological and ecological phenomena change in space and over time. My special interest is animal movement ecology and the mechanisms behind the patterns of movement we observe. Most of the time I work on ecological questions about how animals use their environment and the resources in it, using data collected remotely with animal-attached instruments. Marine biology was my first love so I will always have a soft spot for marine systems, especially movement of large marine vertebrates, but I work on all sorts of tracking data and also some non-tracking data.”

Theoni has also recently been published in Methods in Ecology and Evolution. Her article ‘Analysis of animal accelerometer data using hidden Markov model‘ appeared in the February issue of the journal (and provided the cover image). In the paper, the authors provide the details necessary to implement and assess a hidden Markov Model in both the supervised and unsupervised learning contexts and discuss the data requirements of each case. Another of Theoni’s articles has just been accepted for publication in Frontiers in Zoology. ‘Evidence for a postreproductive phase in female false killer whales (Pseudorca crassidens)‘ investigates the evidence for postreproductive lifespan (PRLS) in the false killer whale, using a quantitative measure of PRLS and morphological evidence from reproductive tissue.

Daniele Silvestro

“I am a computational biologist and my research focuses on (macro)evolution and the development of new probabilistic models to better understand it. I am interested in the implementation of Bayesian algorithms to model evolutionary processes such as phenotypic trait evolution and species diversification and extinction. I am also interested in historical biogeography and in particular in the estimation of dispersal rates and biotic connectivity between geographic areas. A lot of my work involves developing new models and algorithms and implementing them in computer programs. I have been using both phylogenetic data and fossil occurrences to infer deep time evolutionary dynamics and I am keen to see an improved integration between paleontological and neontological data in evolutionary research.”

In his most recent article – ‘Bayesian estimation of multiple clade competition from fossil data‘ – Daniele and his co-authors explore the properties of the existing Multiple Clade Diversity Dependence implementation, which is based on Bayesian variable selection, and introduce an alternative parameterisation based on the Horseshoe prior. He was also one of the authors of ‘Mammal body size evolution in North America and Europe over 20 Myr: similar trends generated by different processes‘, published in Proceedings of the Royal Society B earlier this year.

We are thrilled to welcome Simon, Graziella, Theoni and Daniele to the Associate Editor Board and we look forward to working with them over the coming years.

2016 Robert May Prize Winner: Gabriella Leighton

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 2016 winner is Gabriella Leighton, for her article ‘Just Google it: assessing the use of Google Images to describe geographical variation in visible traits of organisms.

‘Just Google it’ marks an important step in converting ecology to an armchair science. Many species (e.g. owls, hawks, bears) are difficult, time-consuming, expensive and even dangerous to observe. It would be a lot easier if we didn’t have to spend time, energy and risk lives having to observe organisms in the field! Continue reading

New Associate Editors

Today we are welcoming two new people to the Methods in Ecology and Evolution Associate Editor Board. Pierre Durand is joining us from the University of the Witwatersrand (South Africa) and Andrew Mahon joins from Central Michigan University (USA). You can find out more about Pierre and Andrew below.

Pierre Durand

Pierre Durand

“My research is broadly focussed on the evolution of complexity. Many of my projects are related to the evolutionary ecology of programmed cell death (PCD) in unicellular organisms; how PCD impacts microbial communities; and how the philosophy of levels of selection informs our understanding of PCD evolution. I have also examined other aspects of complexity evolution such as the origin of life and group formation in unicellular chlorophytes in response to predation. The model organisms I typically use are phytoplankton. With specific reference to submissions to Methods in Ecology and Evolution, I have used a range of methods in my research, including general cell and molecular biology tools, biochemical assays, microscopy, flow cytometry, bioinformatics and computational algorithms.”

The most current projects in Pierre’s laboratory concern: programmed cell death evolution and complexity in microbial communities; changes in phytoplankton abundance and diversity in harmful algal blooms, led by PhD candidate Andrew Ndhlovu (“A red tide forming dinoflagellate Prorocentrum triestinum: identification, phylogeny and impacts on St Helena Bay, South Africa” in review in Phycologia); and the genomics of the four-celled chlorophyte Tetrabaena socialis, led by PhD candidate Jonathan Featherson.

Andrew Mahon

Andrew Mahon

“I’m a molecular ecologist who uses genetic and genomic tools to ask questions ranging from surveillance and monitoring to biodiversity and phylogeography.  My work includes development of novel molecular detection tools and metabarcoding applications for aquatic invasive species.  I’m also interested in applying molecular tools to ask questions related to the evolution and biodiversity of benthic marine invertebrates in Antarctica.”

Andrew has recently been published in the journal Research Ideas and Outcomes (‘DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe‘) and in Environmental Science and Technology (‘Influence of Stream Bottom Substrate on Retention and Transport of Vertebrate Environmental DNA‘). He also has a manuscript in press with Ecology and Evolution (‘Geographic structure in the Southern Ocean circumpolar brittle star Ophionotus victoriae (Ophiuridae) revealed from mtDNA and single-nucleotide polymorphism data‘).

We are thrilled to welcome Pierre and Andrew to the Associate Editor Board and we look forward to working with them over the coming years.

A Homage to EC Pielou: One of the 20th Century’s Most Accomplished Scientists

Post provided by Daniel Simberloff, Nathan Sanders and Pedro Peres-Neto

Evelyn Chrystalla ‘E.C.’ Pielou. © Sharon Niscak

Evelyn Chrystalla ‘E.C.’ Pielou. © Sharon Niscak

Evelyn Chrystalla ‘E.C.’ Pielou (February 20, 1924 – July 16, 2016) – a towering figure in ecology – was a key pioneer in the incorporation of statistical rigor into biogeography and ecology. She devised many important statistical hypotheses tests for spatial arrangements and patterns ranging in scale from individual plants in a field through to elevational zonation of vegetation to ranges of groups of species distributed over regional through to continental-scale ranges. Her research has provided the impetus for biogeographical analyses for generations.

She published ten books, including several long after her formal retirement in 1988. Her book Biogeography (1979) is a masterpiece. It covers historical biogeography (including inferences from cladograms, which were just beginning to be a hot topic at that time) and ecological biogeography with keen insight and treats topics like long-distance dispersal (that had largely been the subject of just-so stories) with her characteristic statistical rigor. Her books on mathematical ecology have a strong emphasis on models of spatial pattern and ways to estimate biodiversity, and her methods – including the famous Pielou‘s evenness index – are still widely used. Continue reading

Movement Ecology: Stepping into the Mainstream

Post provided by Theoni Photopoulou

“Movement is the glue that ties ecological processes together”
from Francesca Cagnacci et al. 2010

CTD-SRDL telemetry tags being primed for deployment. ©Theoni Photopoulou

CTD-SRDL telemetry tags being primed for deployment. ©Theoni Photopoulou

Movement ecology is a cross-disciplinary field. Its main aim is to quantitatively describe and understand how movement relates to individual and population-level processes for resource acquisition and, ultimately, survival. Today the study of movement ecology hinges on two 21st century advances:

  1. Animal-borne devices/tags (biologging science, Hooker et al., 2007) and/or remote sensing technology to quantify movement and collect data from remote or otherwise challenging environments
  2. Computational power sufficient to manipulate, process and analyse substantial volumes of data

Although datasets often involve small numbers of individuals, each individual can have thousands – sometimes even millions – of data points associated with it. Study species have tended to be large birds and mammals, due to the ease of tag attachment. However, the trend for miniaturisation of tags and the development of remote detection technologies (such as radar, e.g. Capaldi et al., 2000), have allowed researchers to track and study ever smaller animals. Continue reading

We Shall Overcome, Someday! Tips for Breaking Academia’s Glass Ceiling

Post provided by Nibedita Mukherjee

Breaking academia’s glass ceiling

Breaking academia’s glass ceiling

Women in academia are special. This isn’t because of their abundance and diversity (or lack of it in some circles) but rather because of the challenges faced by women. As an early career woman researcher, I have had the privilege of knowing and learning from some incredibly inspirational women scientists. In this post – peppered with the lyrics of Joan Baez – we will meet three of these exceptional scientists working in three different realms (terrestrial, estuarine and marine). I hope that their strengths will be as inspirational to others – as they have been to me – and that in the years to come, we, as women, shall overcome the glass cliffs and glass ceilings of academia.

We’ll Walk Hand in Hand, Some Day #Equality

In the terrestrial realm of tropical forests, researchers often have to work with government officials (for instance, the forest department). Challenges of gender equality can be particularly stark in these workplaces. A key challenge for women in such a setting is not being considered a professional. Female researchers are far too often underestimated: lecturers assumed to be trainees, post-doctoral researchers mistaken for students. Continue reading

Carson’s Call: An Inspiration for Ecologists Working in a Post-Truth World

Post provided by Will Pearse

Rachel Carson (1940) Fish & Wildlife Service employee photo.

Rachel Carson (1940) Fish & Wildlife Service employee photo.

I can’t think of a more inspirational and influential ecologist than Rachel Carson. Nearly fifty years ago she released a book called Silent Spring, which argued that pesticides such as DDT were cascading up through food chains causing the death or sterilisation of birds and other animals. The publication of her book provoked public debate, likely in part because it was serialised in The New Yorker, and led to a paradigm shift in US and (arguably) global pest control policy.

With the full support of the scientific community to verify her facts and arguments, she was able to defeat the chemical industry’s backlash and galvanise public opinion in her favour. The 2005 Stockholm Convention, in which DDT was banned from agricultural use, would likely have never happened if it were not for her work.

“In a post-truth world where trust in the scientific process is being eroded almost daily, Rachel Carson is a perfect example of how we can speak out and be heard while still being scientists.”

Continue reading

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

New Associate Editor: Marie Auger-Méthé

Today, we are pleased to be welcoming a new member of the Methods in Ecology and Evolution Associate Editor Board. Marie Auger-Méthé joins us from Dalhousie University in Canada and you can find out a little more about her below.

Marie Auger-Méthé

Marie Auger-Méthé

“I am broadly interested in developing and applying statistical tools to infer behavioural and population processes from empirical data. My work tends to focus on marine and polar mammals, but the methods I develop are often applicable to a wide range of species and ecosystems. My recent work has centred on modelling animal behaviour using movement data and I generally analyse data with spatial and/or temporal structure.”

Marie has been reviewing for Methods in Ecology and Evolution for a few years and has contributed articles to some of the other journals of the British Ecological Society too. Earlier this month, her article titled ‘Evaluating random search strategies in three mammals from distinct feeding guilds‘ was published in the Journal of Animal Ecology. Continue reading