Getting Serious About Transposable Elements

Post Provided by: Gabriel Rech and José Luis Villanueva-Cañas

So Simple yet so Complex

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

Why Soft Sweeps from Standing Genetic Variation are More Likely than You May Think

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 soft sweep.
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.”

This video is based on the Open Access article ‘Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation by Hermisson and Plennings in the ‘How to Measure Natural Selection‘ Special Feature.

 

New Associate Editors

Over the next few weeks we will be welcoming three new Associate Editors to Methods in Ecology and Evolution. Susan Johnston (University of Edinburgh, UK) became a member of the Associate Editor Board on Monday 5 October. She will be joined on 19 October by Natalie Cooper (Natural History Museum, London, UK) and finally by Luísa Carvalheiro (University of Brasília, Brazil) on 2 November. You can find out more about all three of our new Associate Editors below.

Susan Johnston

Susan Johnston“My research focuses on using genomic information to understand evolution in natural populations. I adapt mixed model approaches to determine the genetic architecture of interesting traits (e.g. estimating heritability, genome-wide association studies, outlier analyses) to examine its relationship with fitness or importance in local adaptation. I am interested in the potential of affordable genomics to answer evolutionary and ecological questions in wild systems, and how to deal with various statistical issues arising from such studies in small and/or structured populations.”

Susan’s most recently published article is ‘Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population‘, co-authored with T. Aykanat, P. Orell, E. Niemelä, J. Erkinaro and C.R. Primmer. The findings suggest that different evolutionary processes affect sub-populations of Atlantic salmon and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence. This article was published in Molecular Ecology.

Natalie Cooper

Natalie Cooper“I am an evolutionary biologist, focusing mainly on macroevolution and macroecology. My interests include phylogenetic comparative methods, morphological evolution, using museum specimens in research, and integrating neontological and palaeontological data and approaches for understanding broad-scale patterns of biodiversity.”

Natalie has recently been published in Molecular Phylogenetics and Evolution (‘Effects of missing data on topological inference using a Total Evidence approach‘ with T. Guillerme) and in Evolution (‘Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT)‘ with C.L. Nunn). She was also a speaker at the Methods in Ecology and Evolution 5th Anniversary Symposium. Her presentation, ‘Limitations of Phylogenetic Comparative Methods‘, is freely available on YouTube.

Luísa Carvalheiro

Luisa Carvalheiro“My research focuses on community ecology & conservation. I have particular interest in the study of dynamics of biodiversity through time and space; and on the evaluation of how such biotic changes affect ecosystem functioning and ecosystem services, considering how the complex network of ecological interactions in which species are integrated mediates such changes.”

Earlier this year Luísa’s article ‘Susceptibility of pollinators to ongoing landscape changes depends on landscape history‘ (with J. Aguirre-Gutiérrez, J.C. Biesmeijer, E.E. van Loon, M. Reemer, and M.F. Wallis De Vries) was published in Diversity and Distributions. The article emphasizes the limited value of a one-size-fits-all biodiversity conservation measures and highlights the importance of considering landscape history when planning biodiversity conservation actions. This article is Open Access. Luísa was also the lead author of ‘The potential for indirect effects between co-flowering plants via shared pollinators depends on resource abundance, accessibility and relatedness‘ an Open Access article published in Ecology Letters last year.

We are thrilled to welcome Susan, Natalie and Luísa to the Associate Editor Board and we look forward to working with them over the coming years.