We recently published a paper in Molecular Ecology Resources describing a method to determine ploidy in mixed ploidy samples from low to modest coverage GBS-like data (paper). This relies on both estimates of heterozygosity and allele specific read depth. The method we describe is implemented in the R package, gbs2ploidy. You can read more about it in this informative blog from the Molecular Ecologist.
Lauren’s paper on patterns and rates of gene flow within four narrowly endemic, spring-associated species is now out in Freshwater Biology. An image from the study of the amphipod Stygobromu made the cover (see above). The paper makes nice use of approximate Bayesian computation to contrast rates and models of gene flow among distantly related sympatric taxa.
Vladmir Nabokov is probably best known for his work in fiction (he wrote Lolita, among other things), but he was also a Lepidopterist. In fact, he was responsible for much of the early systematic work on the butterflies we study, Lycaeides. Lauren’s book (she contributed a chapter, Stephen Blackwell and Kurt Johnson were the editors) connects his work in art and literature to his science. Its out now (you can get it here)! Her chapter highlights how our own research has been influenced by Nabokov. Vladmir Lukhtanov wrote a nice review of the book for Nature.
Molecular Ecology published a special issue on detecting selection in natural populations. It included our paper, which introduced a new method for estimating selection from genetic time-series data (allele frequencies), along with interesting papers on detecting polygenic selection (Stephan 2016), promises of combing experimental evolution with population genomics (Bailey & Bataillon 2016), and considerations for conducting genome scans (Haasl & Payseur 2016) (along with many interesting empirical papers). Check it out!
Stacy Krueger-Hadfield wrote a nice blog piece for The Molecular Ecologists covering some of our work on modelling uncertainty in DNA sequence data. As she notes, we have long-advocated for propagating uncertainty in genotype into inferences of population genetic parameters (e.g., measures of differentiation, introgression, etc.). This provides more honest measures of overall uncertainty and allows one to take advantage of lower-coverage sequence data. Check out her post here.
We seek a Master’s student to conduct research on evolutionary responses to climate change. The student will be co‐advised by Peter Adler and Zach Gompert at Utah State University. Together we will investigate changes in the genetic diversity of two perennial grass species in a long‐term precipitation manipulation experiment in an eastern Idaho sagebrush steppe. We will compare the experimental responses with patterns across an elevation and precipitation gradient. Field sampling will begin in May, 2016. Stipend support will consist of both research and teaching assistantships. To apply, please email a 1) cover letter, 2) CV, 3) description of research experience, and 4) contact information for three references to Peter Adler (email@example.com) by Dec. 1.
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.