Occupancy surveys are widely used in ecology to study wildlife and plant habitat use. To account for imperfect detection probability many researchers use occupancy models. But occupancy probability estimates for rare species tend to be biased because we’re unlikely to observe the animals at all and as a result, the data aren’t very informative. In their new article – ‘Occupancy surveys with conditional replicates: An … Continue reading Conditional Occupancy Design Explained
Rather than conduct an aquatic roll call with nets to know which fish reside in a particular body of water, scientists can now use DNA fragments suspended in water to catalog invasive or native species.
“We’ve sharpened the environmental DNA (eDNA) tool, so that if a river or a lake has threatened, endangered or invasive species, we can ascertain genetic detail of the species there,” said senior author David Lodge, the Francis J. DiSalvo Director of the Atkinson Center for a Sustainable Future at Cornell, and professor of ecology and evolutionary biology. “Using eDNA, scientists can better design management options for eradicating invasive species, or saving and restoring endangered species.” Continue reading “Refined DNA Tool Tracks Native and Invasive Fish”
New method faster, more efficient and less damaging to the environment
A team of researchers from the University of Wollongong (UOW) and the University of Tasmania has developed a new method for assessing the health of fragile Antarctic vegetation using drones, which they say could be used to improve the efficiency of ecological monitoring in other environments as well.
The researchers have written about their method in an article published in Methods in Ecology and Evolution, a scientific journal of the British Ecological Society.
This issue contains three Applications articles (one of which is Open Access) and one additional Open Access article. These four papers are freely available to everyone, no subscription required.
– BioEnergeticFoodWebs: An implementation of Yodzis & Innes bio-energetic model, in the high-performance computing language Julia. This package can be used to conduct numerical experiments in a reproducible and standard way.
–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.
A long standing research topic in evolutionary biology is the genetic basis of adaptation. In other words, how does a novel trait appear (or spread) in response to an environmental change? Despite the rapid advances in sequencing over the last two decades, we have only been able to fully characterize a few adaptations.
As stated by Richard Dawkins in Climbing Mount Improbable, while natural selection is a very simple process, modeling natural selection and determining its causes, effects and consequences is an extremely difficult task. Also, most of our efforts so far have been focused on just one type of genetic variation: single nucleotide polymorphisms (SNPs). Other types of variations such as transposable element (TE) insertions have received much less attention. Paradoxically, some great examples of the role of TEs in adaptation have been right under our noses the whole time, in basic biology textbooks. Continue reading “Getting Serious About Transposable Elements”
We coined the term “soft sweeps” in 2005. The term has since become widely used, though not everyone uses the term in the same way. As part of the ‘How to Measure Natural Selection‘ Special Feature in Methods in Ecology and Evolution, we attempt to clarify what “soft sweep” means and doesn’t mean. For example, not every sweep from standing genetic variation is necessarily a … Continue reading Why Soft Sweeps from Standing Genetic Variation are More Likely than You May Think
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 “Evolutionary Quantitative Genetics: Virtual Issue”
Britain’s smallest bird species, the goldcrest, is being hit hard by cold winters, new analysis methods developed by researchers at the University of St Andrews have revealed.
The data analysis techniques, published today in Methods in Ecology and Evolution, take a longer term view over multiple locations and for a period of several years, compared to previous studies.
This call for tips and tricks has now closed. The Guide to Reproducible Code in Ecology and Evolution has been published and is freely available to everyone. 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 … Continue reading BES Guide to Reproducible Code: Tips and Tricks Needed
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.
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.”
Methods Blog 