In January 2018, Methods in Ecology and Evolution launched a Policy on Publishing Code. The main objective of this policy is to make sure that high quality code is readily available to our readers. set out four key principles to help achieve this, as well as explaining what code outputs we publish, giving some examples of things that make it easier to review code, and giving some advice on how to store code once it’s been published.
The BES Microbial Ecology Special Interest Group is running a workshop today (Thursday 2 November) on Novel Tools for Microbial Ecology. To compliment this workshop, Xavier Harrison has edited a Virtual Issue of the best Methods in Ecology and Evolution articles on advances in methods of studying microbial evolution and ecology from the past few years.
Advances in Next-Generation Sequencing (NGS) technology now allow us to study associations between hosts and their microbial communities in unprecedented detail. However, studies investigating host-microbe interactions in the field of ecology and evolution are dominated by 16S and ITS amplicon sequencing. While amplicon sequencing is a useful tool for describing microbial community composition, it is limited in its ability to quantify the function(s) performed by members of those communities. Characterising function is vital to understanding how microbes and their hosts interact, and consequently whether those interactions are adaptive for, or detrimental to, the host. The articles in this Virtual Issue cover a broad suite of approaches that allow us to study host-microbe and microbe-microbe interactions in novel ways.
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) aspectsof understanding the nuts and bolts of evolutionary change.Continue reading →
‘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 →
It’s not easy to characterise the local environment of species living in mountains because these habitats are highly heterogeneous. At a large scale, we typically assume that temperature varies with altitude, but at a local scale, we understand that exposure to wind or being in the shade has a great influence on climatic conditions. If you go from the south-facing to the north-facing side of a mountain, it can be easily 5°C colder. If we can feel that, so can the organisms that live up there. Plants in particular are submitted to tremendous climatic variations over a year. What we want to know is: how did they adapt to these climatic variations and how localised is their adaptation?
Overcoming the Challenges of Measuring Local Adaptation
We don’t know much about how organisms adapt locally because it’s so difficult to measure the environmental conditions that these plants are facing. Existing weather stations can’t capture micro-habitat conditions because they are few and far between. What we can do instead, is use topographic models of mountains to model their environment. After all, if orientation, slope or shade have an impact on climatic conditions, why couldn’t we use them to model local variations in temperature for example? Continue reading →
I have always loved the Blue Marble image of Earth from the Apollo 17 mission, yet a large part of my science is focused on experimental responses at the scale of meter squared grassland plots or even individual grass plants. While I spent my early career wanting to be able to say something important about regional or global processes, I found myself feeling like generating any experimental insights into processes and ecosystem responses at larger scales would be an impossible fiction.
As a postdoc, I had the opportunity to do a multi-site study across a north-south precipitation gradient in California and jumped at it. Among other questions, I decided to ask about whether plants and insects varied similarly across sites in response to replicated experimental treatments. Yet, the idea of actually sampling – and then processing samples from – more than about four sites for more than a year or two was utterly daunting. Continue reading →
To truly understand how species’ distributions vary through space and time, biogeographers often have to make use of analytical techniques from a wide array of disciplines. As such, these papers cover advances in fields such as evolutionary analysis, biodiversity definitions, species distribution modelling, remote sensing and more. They also reflect the growing understanding that biogeography can include experiments and highlight the increasing number of software packages focused towards biogeography.
This Virtual Issue was compiled by Methods in Ecology and Evolution Associate Editors Pedro Peres-Neto and Will Pearse (both of whom are involved in the conference). All of the articles in this Virtual Issue are free for a limited time and we have a little bit more information about each of the papers included here: Continue reading →
How many samples do you hope to collect on your next field assignment? 50, 100 or 1000? How about billions. It may seem overly optimistic, but that’s the reality when using Light Detection and Ranging, or LiDAR.
LiDAR works on the principle of firing hundreds of thousands of laser pulses a second that measure the distance to an intercepting surface. This harmless barrage of light creates a highly accurate 3D image of the target – whether it’s an elephant, a Cambodian temple or pedestrians walking down the street. LiDAR has made the news over recent years for its ability to unearth ancient temples through thick jungle, but for those of us with an ecological motive it is the otherwise impenetrable cloak of vegetation which is of more interest.
It’s very hard to make sensible choices without sensible information. When it comes to actions around changing land use and its ecological impact though, this is often what we are forced to do. If we want to reduce the impact of human activities on natural ecosystems, we need to know how much change has already occurred and how altered an ecosystem might be from its “natural” state.
Working out which parts of the landscape have been changed and mapping the absence of natural vegetation is an achievable (though onerous) task. However, moving beyond this binary view of the world is a huge challenge. Pretty much all habitat has been modified by human influences to some extent – by, for example, wood extraction, the introduction of invasive species or livestock grazing. This means that a lot of the apparently native habitat is no longer capable of supporting its full complement of native biodiversity. Continue reading →
In the UK, National Tree Week (26 November – 4 December) celebrates tree planting within local communities. The latest BES cross-journal Virtual Issue contains recent papers that highlight the global importance of trees and forests as habitat – for species from insects to primates – and in meeting human needs for fuel and agriculture. The selected papers also demonstrate novel methods scientists are using to study trees and forests.
National Tree Week is the UK’s largest tree celebration. It was started in 1975 by the Tree Council and has grown into an event that brings hundreds of organisations together to mark the beginning of Britain’s winter tree planting season.
Landscape connectivity is important for the ecology and genetics of populations threatened by climate change and habitat fragmentation. To begin our Virtual Issue Rayfield et al. present a method for identifying a multipurpose network of forest patches that promotes both short- and long-range connectivity. Their approach can be tailored to local, regional and continental conservation initiatives to protect essential species movements that will allow biodiversity to persist in a changing climate. The authors illustrate their method in the agroecosystem bordered by the Laurentian and Appalachian mountain ranges, that surrounds Montreal.