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 →
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.
Despite how far modelling has taken us in science, the use of models remains controversial. Modelling covers a huge range of common practices, from scaled models of ships to determine the shape that will have the least resistance to water to complex, comprehensive ‘models of everything’. A great example of the latter is the Earth System Model. This model aims to understand the changes in global climate by taking into account the interaction between physical climate, biosphere, the atmosphere and the oceans. Basically, a model of how the Earth works.
The controversy in the use of modelling resides in how accurately the model describes reality and the level of confidence we have in its outputs. The first argument can be a bit counter-intuitive: sometimes, a very simple model can be a great predictor. Actually, the conventional view in ecology is that simple models are more generalisable than complex models, although this view is being challenged. However, the level of confidence, or the level of uncertainty, that we have in the outputs of the model is a crucial point. We need to be able to accurately determine our levels of uncertainty if we want people to trust our models. Continue reading →
In this video, the authors explore the potential of DNA metabarcoding to access stream health using macroinvertebrates. They compared DNA and morphology-based identification of bulk monitoring samples from 18 Finnish stream ecosystems. DNA-based methods show higher taxonomic resolution and similar assessment results as currently used morphology-based methods. Their study shows that the tested DNA-based methods integrate well with current approaches, but further optimisation and validation of DNA metabarcoding methods is encouraged.
Time flies… in the blink of an eye! And even more so in science. The molecular lab work we were used to two decades ago seems like ancient history to today’s PhD students. The speed of change in sequencing technology is so overwhelming that imagination usually fails to foresee how our daily work will be in 10 years’ time. But in the field of biodiversity assessment, we have very good clues. Next Generation Sequencing is quickly becoming our workhorse for ambitious projects of species and genetic inventories.
One by One Approach to Studying Biodiversity
For decades, most initiatives measured biodiversity in the same way: collect a sample of many individuals in the field, sort the specimens, identify them to a Linnaean species one at a time (if there was a good taxonomist in the group which, unfortunately, it is kind of lucky these days!), and count them. Or, if identification was based on molecular data, the specimen was subject to DNA extraction, to sequence one (or several) short DNA markers. This involved countless hours of work that could be saved if, instead of inventorying biodiversity specimen-by-specimen, we followed a sample-by-sample approach. To do this now, we just have to make a “biodiversity soup”.
Biodiversity assessment based on morphological identification and/or Sanger sequencing (“The one-by-one approach”)
Traditional stream assessment using visual identification of indicator species is time-consuming, expensive and procedures are seldom standardised. Especially small organisms may look similar and misidentifications happen frequently. Using a genetic method to identify the species these concerns are not an issue, as even small organisms can be securely identified using a DNA marker. Continue reading →