In reality, code is often poorly commented (or not commented at all!), hard to reuse for other projects, and difficult to interpret. To add to that, most code isn’t actively maintained, so users are on their own if they try to commandeer it for new purposes. Further, ecologists with little or no programming knowledge are unlikely to benefit from methods that exist only as poorly documented code. In a positive development, some new methods are accessible through software with graphic user interfaces (GUIs) developed by programmers spending significant time and effort. But too often these end up as tools with flashy controls and insufficient instruction manuals. Continue reading →
Traditional conservation biology has been dominated by quantitative data (measured in numbers) but today it frequently relies on qualitative methods such as interviews and focus group discussions. The aim of the special issue is to help researchers decide which techniques are most appropriate for their study, and improve the “methodological rigour” of these techniques. Continue reading →
The availability and accessibility of multispectral and radar satellite remote sensing (SRS) imagery are at an unprecedented high. However, despite the benefits of combining multispectral and radar SRS data, data fusion techniques, including image fusion, are not commonly used in biodiversity monitoring, ecology and conservation. To address this, the authors provide an overview of the most common SRS data fusion techniques, discussing their benefits and drawbacks, and pull together case studies illustrating the added value for biodiversity research and monitoring.
More than anything else, the phenotype of an organism determines how it interacts with the environment. It’s subject to natural selection, and may help to unravel the underlying evolutionary processes. So shape traits are key elements in many ecological and biological studies.
Commonly, basic parameters like distances, areas, angles, or derived ratios are used to describe and compare the shapes of organisms. These parameters usually work well in organisms with a regular body plan. The shape of irregular organisms – such as many plants, fungi, sponges or corals – is mainly determined by environmental factors and often lacks the distinct landmarks needed for traditional morphometric methods. The application of these methods is problematic and shapes are more often categorised than actually measured.
As scientists though, we favour independent statistical analyses, and there’s an urgent need for reliable shape characterisation based on numerical approaches. So, scientists often determine complexity parameters such as surface/volume ratios, rugosity, or the level of branching. However, these parameters all share the same drawback: they are delineated to a univariate number, taking information from one or few spatial scales and because of this essential information is lost. Continue reading →
Today we are welcoming another two Associate Editors to the Methods in Ecology and Evolution. Just like the seven AEs who joined last week, Michael Matschiner (of the University of Basel, Switzerland) and Tiago Bosisio Quental (of the University of São Paulo, Brazil) were both invited to work with the journal following our open call earlier this year. You can find out more about both of them below.
“I am an evolutionary biologist interested in the processes that drive speciation and generate biodiversity. To learn about these processes, I use phylogenetic divergence-time estimation based on genome sequences and the fossil record. Since both of these data sources do not usually conform to expectations in standard phylogenetic workflows (no recombination, no hybridization, no sampling bias), much of my work involves method development to assess the impact of model violations, and to account for them in phylogenetic reconstruction.”
Tiago Bosisio Quental
“I am interested on understanding spatial and temporal patterns of biodiversity and the mechanisms involved in generating species diversity. I have a particular interest in mammals, but my research interests are not limited to a specific taxonomic group but are instead motivated by a range of questions and structured around them. At the moment, I am particularly interested in understanding the role of biotic interactions on biodiversity changes in deep time. The main tools used to approach those questions are molecular phylogenies, fossil record, ecological data and numerical simulation.”
We are thrilled to welcome Michael and Tiago to the Associate Editor Board and we look forward to working with them over the coming years.
This double-sized issue contains three Applications articles and two Open Access articles. These five papers are freely available to everyone, no subscription required.
–Phylogenetic Trees: The fields of phylogenetic tree and network inference have advanced independently, with only a few attempts to bridge them. Schliep et al. provide a framework, implemented in R, to transfer information between trees and networks.
–Emon: Studies, surveys and monitoring are often costly, so small investments in preliminary data collection and systematic planning of these activities can help to make best use of resources. To meet recognised needs for accessible tools to plan some aspects of studies, surveys and monitoring, Barry et al. developed the R package emon, which includes routines for study design through power analysis and feature detection.
–Haplostrips: A tool to visualise polymorphisms of a given region of the genome in the form of independently clustered and sorted haplotypes. Haplostrips is a command-line tool written in Python and R, that uses variant call format files as input and generates a heatmap view.
One of the main causes behind biodiversity loss is the reduction and fragmentation of natural habitats. The conversion of natural areas into agricultural, urban or other human-modified landscapes often leaves wild species confined to small and isolated areas of habitat, which can only support small local populations. The problem with small, isolated populations is that they are highly vulnerable to extinction caused by chance events (such as an epidemic or a natural disaster in the area), or by genetic erosion (dramatic loss of genetic diversity that weakens species and takes away their ability to adapt to new conditions).
On top of that, we now have the added concern of climate change, which is altering environmental conditions and shifting habitats to different latitudes and altitudes. To survive in the face of these changes, many species need to modify their geographical distribution and reach new areas with suitable conditions. The combination of mobility (a biological property of species) and the possibility of spatial movement (a physical property of the landscape) is critically important for this. Continue reading →
Before I started my NERC Valuing Nature Placement in April 2017, I’d never done interdisciplinary work. I had been thinking about it for a while though, when I read on Twitter that the Valuing Nature Programme were launching their placement scheme for 2017. I had already been in touch with my prospective hosts – Hilary Graham, Department of Health Science, and Piran White, Environment Department, both at the University of York – but the launch of the scheme galvanised our interest. We put together our application and were delighted to receive funding. So, what is that we set out to do?
Piran, Hilary and I had already been talking about projects focusing on knowledge transfer, particularly around collaborative work to tackle antimicrobial resistance. Valuing Nature was the perfect fit for what we wanted to do. The programme aims to further our understanding of nature in valuation analyses and decision making by building an interdisciplinary research community capable of working across the natural, biological and social sciences, as well as the arts and humanities. Interdisciplinarity is integral to the programme. Continue reading →
–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.
To me, the ‘citizen scientist’ label feels a little patronising – conveying an image of people co-opted en masse for top-down, scientist-led, large-scale biological surveys. That said, scientist-led surveys can offer valid contributions to conservation and the documentation of the effects of climate change (among other objectives). They also engage the public (not least children) in science, although volunteers usually have an interest in natural history and science already. For me though, the real excitement comes in following a bottom-up path: making my own discoveries and approaching scientists for assistance with my projects.
Robert Colwell at the Boreas Pass in Colorado, USA
ROB: I grew up on a working ranch in the Colorado mountains, surrounded on three sides by National Forest and a National Wilderness Area. My mother, an ardent amateur naturalist, taught me and my sister the local native flora and fauna and our father instilled a respect for the land in us. For my doctoral research at the University of Michigan, I studied insect biodiversity in Colorado and Costa Rica at several elevations. The challenges of estimating the number of species (species richness) and understanding why some places are species-rich and others species-poor has fascinated me ever since. Continue reading →