Francesco de Bello describes the main elements of the method he has recently published in Methods in Ecology and Evolution. The method aims at decoupling and combining functional trait and phylogenetic dissimilarities between organisms. This allows for a more effective combination of non-overlapping information between phylogeny and functional traits. Decoupling trait and phylogenetic information can also uncover otherwise hidden signals underlying species coexistence and turnover, by revealing the importance of functional differentiation between phylogenetically related species.
In the video Francesco visually represents what the authors think their tool is doing with the data so you can see its potential. This method can provide an avenue for connecting macro-evolutionary and local factors affecting coexistence and for understanding how complex species differences affect multiple ecosystem functions.
“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.”
“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.”
BACIPS (Before-After Control-Impact Paired Series) is probably the best-known and most powerful approach to detect and quantify human interventions on ecosystems. In BACIPS designs, Impact and Control sites are sampled simultaneously (or nearly so) multiple times Before and After an intervention. For each sampling survey conducted Before or After, the difference in the sampled response variable (e.g. density) is calculated. Before and After differences are then compared to provide a measure of the effect of the intervention, assuming that the magnitude of the induced change is constant through time. However, many interventions may not cause immediate, constant changes to a system.
We developed a new statistical approach – called Progressive-Change BACIPS (Before-After Control-Impact Paired-Series) – that extends and generalises the scope of BACIPS analyses to time-dependent effects. After quantifying the statistical power and accuracy of the method with simulated data sets, we used marine and terrestrial case studies to illustrate and validate their approach. We found that the Progressive-Change BACIPS works pretty well to estimate the effects of environmental impacts and the time-scales over which they operate.
The following images show the diversity of contexts in which this approach can be undertaken.
Moorea is an island located in French Polynesia. It’s known for its extraordinary marine biodiversity, but also for the great, natural spatial and temporal variability due to recurrent external forces. This place, and the statistical challenges it represents, has provided us with a wealth of inspiration in formulating our Progressive-Change BACIPS approach to environmental impact assessment.
Unlike classic experimental studies like this one, environmental impacts are not (and often should not) be replicated.
Recurrent disturbances such as Crown-of-Thorns Starfish (Acanthaster planci) outbreaks are important drivers of declines and recoveries in coral reef ecosystems. How can we reliably estimate the effect of local human interventions (for example marine protected areas, MPAs) amid such noise?
The challenge faced by ecologists when conducting impact assessments is to compare the state of the ecosystem in the presence of the intervention with the state of the system that would have existed if the intervention never occurred. This requires scientists to collect data before the intervention.
Here, a scientist is counting fish where a MPA will be implemented using a Diver-Operated Video system. Repeated assessments before enforcement provide an estimate of the spatial variability between the Control and Impact sites in the absence of an effect of the MPA.
A change in the difference in density between the Control and Impact sites after the establishment of the MPA provides an estimate of the local effect of the MPA. This is the BACIPS design.
Progressive-Change BACIPS uses these data to inform the form of the final model. Many models can be tested such as step-change, linear, asymptotic or logistic models – whatever that seems appropriate. This coral reef application was just one of the many possibilities to measure environmental impacts that our tool can reveal when applied to BACIPS data.
We have also applied it to other study contexts – such as the effect of highway construction on the abundance of birds. Here is an Andean condor (Vultur gryphus) flying away after the passage of a car.
This method is also well suited to forest ecosystems, for example to study the effect of increasing tourist visitation on this ancient Araucaria (Araucaria araucana) forest in Chile.
As long as data collected before and after, inside and outside the impacted area, exist Progressive-Change BACIPS is an excellent statistical approach to estimate the effects of environmental impacts.
For the first time, it is possible to integrate at the global scale the results obtained with the most widely used methods to evaluate the “health” of ecosystems using lichens. This is the result of a study now published in the journal Methods in Ecology and Evolution, and represents a fundamental step for this indicator to be considered at the global scale and included in the list of indicators of the United Nations.
Lichens have long been successfully used by scientists as ecological indicators – a kind of environment health thermometer. These complex organisms – the yellow or green taints we often see on the surface of tree trunks – are very sensitive to pollution and changes in temperature and humidity. Evaluating how many lichens, of what kind, and their abundance in a certain ecosystem allows scientists to understand the impact that problems like climate change or pollution have on those ecosystems. 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 →
It’s somehow fitting that the centre piece of an ancient midwinter tradition in Europe – that of decorating and worshipping an evergreen tree – is an ancient seed plant, a conifer. In Europe, we tend to think of conifers as “Christmas trees” – evergreen trees with needles and dry cones, restricted to cold and dry environments – but conifers are much more diverse and widespread than that. There are broad-leaved, tropical conifers with fleshy cones and even a parasitic species that is thought to parasitise on members of its own family!
However, while today’s distribution of conifers is global – spanning tropical, temperate and boreal zones – it is fragmented. The conifer fossil record extends well into the Carboniferous and bears witness to a lineage that was once much more abundant, widespread and diverse. So we can tell that today’s diversity and distribution have been shaped by hundreds of millions of years of speciation, extinction and migration. Continue reading →
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.
Years of research on the evolution of ancient life, including the dinosaurs, have been questioned after a fatal flaw in the way fossil data are analysed was exposed by scientists from the universities of Reading and Bristol.
Studies based on the apparently flawed method have suggested Earth’s biodiversity remained relatively stable – close to maximum carrying capacity – and hinted many signs of species becoming rapidly extinct are merely reflections on the poor quality of the fossil record at that time.
However, new research by scientists at the University of Reading suggests the history of the planet’s biodiversity may have been more dynamic than recently suggested, with bursts of new species appearing, along with crashes and more stable periods.