–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 →
In the review paper we also show under what conditions soft sweeps are likely (e.g., high population-wide mutation rate, multi-locus selection target). Finally, we describe relevant examples in fruitflies, humans and microbes and we discuss future research directions.
The video focuses on one aspect of the paper, which is illustrated in figure 3: “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 →
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.
They showed that the cold temperatures strongly affected breeding numbers of the goldcrest, while in contrast, the song thrush was not affected by the cold, but benefited from wet and mild summers. Continue reading →
Each Guide includes short pieces of advice provided by academics who are familiar with the topic – and this is where you come in. We’re looking for tips and tricks to help Early Career Researchers looking to make their code reproducible and we would like your help.
We’ve set up a Google form with sections that relate to the broad areas that will be covered in our Guide to Reproducible Code:
The guide is intended for people who are fairly new to coding, so please don’t be too technical. There are options to enter three pieces of advice in each section (if you’ve got more tips and tricks, feel free to fill in the form multiple times). We’ll choose the best pieces of advice and publish them in the Guide, along with the name and affiliation of the person who provided them.
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.”
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 →
Ordination and clustering methods are widely applied to ecological data that are non-negative (like species abundances or biomasses). These methods rely on a measure of multivariate proximity that quantifies differences between the sampling units (e.g. individuals, stations, time points), leading to results such as:
Ordinations of the units, where interpoint distances optimally display the measured differences
Clustering the units into homogeneous clusters
Assessing differences between pre-specified groups of units (e.g. regions, periods, treatment–control groups)
In this video, Michael Greenacre introduces his new article, ‘‘Size’ and ‘Shape’ in the Measurement of Multivariate Proximity’, published in Methods in Ecology and Evolution, May 2017. In the context of species abundances, for example, he explains how much a chosen proximity measure captures the difference in “size” between two samples, i.e. difference in overall abundances, and differences in “shape”, i.e. differences in compositions or relative abundances. He shows that the popular Bray-Curtis dissimilarity inevitably includes a part of the “size” difference in its measurement of multivariate proximity.
An Asian, female Senior Editor under 45? Progressive! I have loved Methods in Ecology and Evolution since it appeared in 2010 and am thrilled to have been selected to join Rob, Bob and Jana to help with the journal’s continued development.
OK, so you want to know who the new Senior Editor on the MEE block is. I’m just another scientist, I guess. On the outside, we look different but on the inside, we’re all the same. (OK, perhaps we are a little different, even on the inside, but that makes life and research interesting, right?)
Here’s my academic life history: I did my Bachelors thesis on the systematics/phylogenetics of an obscure group of marine pulmonate slugs with one of the greatest Icelandic biologists I know, Jon Sigurdsson, at the National University of Singapore. I followed this up with an almost-half-year stint at the Museum of Natural Science in Berlin as a “nobody”, digitizing data. Then I won the academic lottery and headed up to Uppsala to do my masters in conservation biology on tropical pollinator diversity, (un)supervised by two amazing supervisors that never met each other, the late Navjot Sodhi (National University of Singapore) and Thomas Elmqvist, now at Stockholm University. Continue reading →