We have developed a new computer program (spatpg) to infer variance effective population size and environment-dependent selection based on genetic time-series data (allele frequencies) from multiple populations. The software, including the source code and manual, can be downloaded here or using the link on our software page. The paper describing the method will be published in a forthcoming special issue in Molecular Ecology on detecting selection in natural populations. The accepted article is available here: Gompert-2015-Molecular_Ecology. We hope to release an updated version of the program that supports parallel processing and low-coverage DNA sequenced data shortly.
I was invited by Lacey Knowles and her lab group to give a seminar at the University of Michigan a few months ago. It was a a fun trip. The seminar was recorded and is now on youtube. It covers our work on hybridization and diversification in Lycaeides butterflies and includes some discussion of statistical approaches for the analysis of admixed populations. Here is a link to the recorded seminar.
Our paper examining constraints on the evolution of host use in the Melissa blue butterfly (Lycaeides melissa) was published in today’s issue of Molecular Ecology. We were interested in the potential for limited genetic variation or genetic trade-offs in performance on different host plants to slow or prevent adaptation to a novel host, in this case alfalfa. To address this question we conducted a massive larval rearing experiment (see the image below) and generated and analyzed partial genome sequences (GBS data) from the larvae (we also sequenced and assembled a draft whole genome for L. melissa to provide genomic context for our results). We found that L. melissa harbor genetic variation for performance on alfalfa and that genetic variants that affect performance on alfalfa do not affect performance on a native host plant. In other words, we found no evidence that genetic trade-offs limit diet breadth (cause host plant specialization) in these butterflies. I think this study shows how genomic data can be used to better test a classic hypothesis in evolutionary genetics.
Alberto de Rosa and Samridhi Chaturvedi joined the lab this fall. They are both PhD students. We are very excited to have them here.
Samridhi earned her B.Sc in Chemistry, Botany, and Zoology from Christ College, Bangalore, India, and then earned her Masters in Applied Microbiology from the Vellore Institute of Technology, India. Her project focused on the genomic basis of Asthma. She then worked at the Indian Institute of Science on molecular phylogenetics of bufonid toads before joining the lab here.
Alberto de Rosa completed his M.Sc in Biodiversity and Evolution from the Università di Bologna in Italy. His thesis was on inter-specific pecking order of mixed groups of birds in semi-natural areas. He has since established an international network of collaborators to investigate the determinants of diversification in island Barn Owls in the Caribbean, with a focus on conservation applications of his research.
Check out our paper analyzing the genomic basis of parallel speciation in stick insects (Timema cristinae) that was just published in Science. We even made the cover! Science also published a related news piece discussing how our study sheds new light on the predictability of evolution. In this study we show that the repeated evolution of reproductive isolation between stick insects on different host plants involved parallel genetic differentiation at only a modest proportion of the genome, and thus genome divergence was mostly idiosyncratic. But, genetic regions that exhibit parallel divergence contain an excess of genes with specific functions, and are likely of central importance for speciation.
Peter Nelson, Robert Olson, and Zach Valois were awarded summer research fellowships (SURCO’s) to work in the lab. This will provide a great opportunity for them to gain lab and field experience. Zach Valois was also awarded research grants from USU (URCO) and from the American Museum of Natural History (Theodore Roosevelt Memorial Fund). Zach presented preliminary findings form his funded project investigating parallel evolution in the Northern Scorpion at the USU Department of Biology Spring 2014 Undergraduate Research Symposium (pictured below).
We were invited to participate in Utah State University’s Science Unwrapped series this April. After listening to a presentation from Paleontologist Mary Schweitzer, kids of all ages visited our booth to view an assortment of arachnids (provided by Zach Valois) and extract DNA from their cheek cells. They created necklaces from their DNA, which they took home with them. We all had a great time.