Issue 8.6: How to Measure Natural Selection

Issue 8.6 is now online!

The April issue of Methods, which includes our latest Special Feature – ‘How to Measure Natural Selection – is now online!

Understanding how and why some individuals survive and reproduce better than others, the traits that allow them to do so, the genetic basis of those traits, and the signatures of past and present selection in patterns of variation in the genome remain at the top of the research agenda for evolutionary biology. This Special Feature – Guest Edited by Jeff Conner, John Stinchcombe and Joanna Kelley – draws together a collection of seven papers that highlight new methodological and conceptual approaches to meeting this agenda.

Three of the ‘How to Measure Natural Selection’ papers – Franklin and Morrissey, Thomson and Hadfield, and Hadfield and Thomson – clarify unresolved aspects of the literature in meaningful and important ways. Following on from this Hermisson and Pennings; Lotterhos et al.; and Villanueva‐Cañas et al. tackle the genomic results of evolution by natural selection: namely, how we can detect natural selection from genomic data? Finally, Wadgymar et al. address the issue of how much we know about the underlying loci or agents of selection.

To use the Editors’ own words, the articles in this issue “deal with how we can detect selection in a way that can be used to predict evolutionary responses, how selection affects the genome, and how selection and genetics underlie adaptive differentiation.”

All of the articles in the ‘How to Measure Natural Selection‘ Special Feature will be freely available for a limited time.
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Editor Recommendation – HistMapR: Rapid Digitization of Historical Land-Use Maps in R

Post provided by Sarah Goslee

For an ecologist interested in long-term dynamics, one of the most thrilling experiences is discovering a legacy dataset stashed away somewhere.

For an ecologist interested in long-term dynamics, one of the most daunting experiences is figuring how to turn that box full of paper into usable data.

The new tool HistMapR, described in ’HistMapR: Rapid digitization of historical land-use maps in R’ by Alistair Auffret and colleagues, makes one part of that task much easier.

Examples of input (©Lantmäteriet) and output maps from (a–b) the District Economic map and (c–d) the Economic map.

Examples of input (©Lantmäteriet) and output maps from (a–b) the District Economic map and (c–d) the Economic map.

Historical maps with coloured areas denoting different land cover or use are a valuable record, but difficult to analyse. This R package automates much of the time-consuming and tedious process of turning paper maps into classified categorical raster maps.

A map is scanned, imported into R, and the software is trained by clicking in different areas of each category. It then automatically classifies pixels based on which colour they are most similar to. The resulting classification is assessed manually. The process can be repeated with slightly different parameters until a good fit is achieved.

The authors found 80-90% agreement between HistMapR classification and manual digitisation (sources of error included clarity of original maps and scan quality). Using HistMapR reduced the time needed for digitising a series of historical land cover maps from two months to two days. Ecologists interested in long-term dynamics should be cheering!

The HistMapR package is available on GitHub and you can find example scripts on Figshare, so you can get right to work.

HistMapR: Rapid digitization of historical land-use maps in R‘ by Auffret et al. is a freely available Applications article (no subscription required).

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.

Issue 8.5

Issue 8.5 is now online!

The May issue of Methods is now online!

This issue contains three Applications articles and two Open Access articles. These five papers are freely available to everyone, no subscription required.

MatlabHTK: A software interface to a popular speech recognition system making it possible for non-experts to implement hidden Markov models for bioacoustic signal processing.

 PrimerMiner: The R package PrimerMiner batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units to reduce biases introduced by the different number of available sequences per species.

 BarcodingR: An integrated software package that provides a comprehensive implementation of species identification methods, including artificial intelligence, fuzzy-set, Bayesian and kmer-based methods, that are not readily available in other packages.

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What Can Penguins Tell Us About Mitochondria? And Vice-Versa!

Post provided by Antoine Stier

Why on earth would someone try to combine field ornithology and mitochondrial biology? They’re so different! However, as I have a general background in both ecology and physiology, I am deeply convinced that physiology can help us to better understand ecology. I also see ways that ecology can help us to better understand physiological processes.

Admittedly, my memories from lectures on the mitochondrial electron transport chain are a little fuzzy – many ecologists and evolutionary biologists might feel the same way. Yet, I discovered the importance of getting over this first negative feeling when realizing the importance of mitochondrial function in shaping both ecological and evolutionary processes. Continue reading

Generating New Ideas in a Conference Setting

Post provided by David Warton

This guy had his eureka moment in the bath (although I have had more success in the shower). ©Dun.can

This guy had his eureka moment in the bath (although I have had more success in the shower). ©Dun.can

A few leading reasons for going to a conference are: to present your work and get feedback on it, to find out what others are doing, to meet collaborators and to network. But a conference can also be a great setting for generating completely new ideas. I find that conferences are one of my most likely places for a “eureka moment”.

Surrounded by researchers working on a range of different problems in interesting and often original ways, I’m encouraged to think about things from a different angle. Idea generation is perhaps one of the main benefits of going to a conference – but is the typical conference format is the best way to facilitate that? Or does it focus too much on giving researchers a platform to report on previous research ideas? Continue reading

Issue 8.4: Technological Advances at the Interface of Ecology and Statistics

Issue 8.4 is now online!

The April issue of Methods, which includes our latest Special Feature – “Technological Advances at the Interface of Ecology and Statistics” – is now online!

This new Special Feature is a collection of five articles (plus an Editorial from Guest Editor David Warton) inspired by the December 2015 Eco-Stats conference at the University of New South Wales in Australia. It shows how interdisciplinary collaboration help to solve problems around estimating biodiversity and how it changes over space and time.

The five articles are based on joint talks given at the conference. They focus on:

As David Warton states in his Editorial, “interdisciplinary collaboration and the opportunities offered by recent technological advances have potential to lead to interesting and sometimes surprising findings, and will continue to be fertile ground for scientists in the foreseeable future”. Meetings like Eco-Stats 15 and Special Features like this one will, hopefully, help to encourage these sorts of collaborative research projects.

All of the articles in the ‘Technological Advances at the Interface of Ecology and Statistics‘ Special Feature will be freely available for a limited time.
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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

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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