New method and software to measure fluctuating selection on polygenic traits

We have new software available to measure selection on polygenic traits based on population-genomic time-series data and a genotype-phenotype map. The method is specifically designed to detect selection that varies in space or time (e.g., because of climatic variation). See our software page or GitHub to access the software. You can read more about the method in our most recent preprint on bioRxiv. Let me know if you have any questions about the method.


Successful MS defense from Alex Rego

Congratulations to Alex Rego for successfully defending his Master’s thesis on the evolutionary dynamics and genetics of adaptation to a marginal host plant by Callosobruchus maculatus.

Rego Defense

Alex has been in the lab since his time as an undergraduate at USU. His thesis work has already resulted in two stellar papers (Rego et al., 2019 and Rego et al. 2020). Alex is now continuous his PhD studies with Rike Stelkens at the University of Stockholm.

Recent vs. ancient hybrids in Lycaeides, new paper at Nature Communications

Our paper on genomic outcomes of recent versus ancient hybridization in Lycaeides butterflies is now out at Nature Communications. Check it out here.


In this paper, we show that ancient admixed butterfly populations have mosaic genomes with ancestry segments that can be predicted (to a reasonable extent) from how natural selection (and recombination) affect the genomes of contemporary hybrids. Thus, our results suggest that natural selection and recombination can affect hybrid genomes in similar ways across disparate time scales and during distinct stages of the origin and collapse of species.

New paper on host adaptation in seed beetles


Our new paper on the genomic basis of host-plant adaptation in the seed beetle, Callosobruchus maculatus is out now. In this study, we combined population-genomic analyses of evolve-and-resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to shed light on how these beetles adapt to and persist on a very low-quality host (lentils). Many factors are involved, including detoxification genes, such as cytochrome P450s and beta-glucosidase. This work was led by (current and former) graduate students in the group, Alex Rego and Sam Chaturvedi, and is part of a special issue on the “Genetic basis of phenotypic variation in Drosophila and other insects”. Check it out along with the full special issue.

PhD position available for fall 2020

The Gompert lab in the Department of Biology at Utah State University (USU) is seeking a highly motivated and enthusiastic PhD student to study the ecological causes and evolutionary genetic consequences of fluctuating selection and contemporary evolution. Research in the lab addresses fundamental questions in evolutionary genetics. We are particularly interested in the genetic architecture of ecologically important traits, the determinants of genetic variation and molecular evolution in natural populations, and the nature and evolution of species boundaries and barriers to gene flow. This specific position is funded through a NSF CAREER award to Gompert. A stipend will be provided via a mixture of teaching and research assistantships. Review of applicants will begin November 25, 2019. The start date for the PhD project is fall 2020.

In the struggle for existence, organisms interact with each other and with their environment. Variation in climate, weather, and species interactions can cause variation in the direction and strength of natural selection. Differences in selection across space cause local adaptation. However, whether seasonal, yearly or longer-term fluctuations in selection are equally important for evolution is unknown. Selection that varies over time can cause rapid evolution. It can also erode or maintain variation for individual traits or genes, but may or may not be an important factor in evolutionary dynamics more broadly. In this NSF-funded project, the Gompert lab will use computer simulations, experiments, and genome sequencing of populations sampled across multiple generations to fill this knowledge gap.

We are looking for a PhD student interested in collaborating on the project. The PhD student will develop computational methods to quantify the prevalence, causes and targets of fluctuating selection from population genomic time-series data. Additional components of the PhD student’s dissertation will be tailored to the student’s interests and background. Possible project include: (i) developing theory on the consequences of fluctuating selection, (ii) studying the evolutionary genomic consequences of fluctuating selection in quasi-natural selection lab experiments (with cowpea seed beetles), or (iii) identifying the causes and consequences of fluctuating selection (or contemporary evolution) using population genomic time-series from natural populations of Lycaeides butterflies.

The successful candidate should have previous training in evolutionary biology, population genetics, applied math and statistics, or computational biology. Some proficiency with R (or other language, e.g., C) or experience working with population genomic data is preferable, but not essential. Students with or without a Master’s degree are encouraged to apply. We welcome and encourage enthusiastic and open-minded applicants from any nation, ethnicity, gender, sexual orientation or socioeconomic class. For more information about the Gompert lab, including a statement of mentoring philosophy and expectations, please visit the lab website at

USU is a public land-grant research university in Logan, Utah (USA). The Department of Biology and USU offer excellent opportunities for education, training, funding, and collaboration. Graduate students in the department have the option of pursuing a PhD in Biology or in the inter-departmental Ecology program. Located in the Rocky Mountains, the Logan area also offers exceptional opportunities for outdoor recreation.

Interested students should e-mail me ( with the following:

1. A cover letter describing the student’s background and training, goals and reasons for pursuing a PhD, and the specific reasons why this opportunity is of exceptional interest.
2. A CV, including contact information for three academic references.
3. A writing sample. This could be in the form of a published or draft manuscript, an undergraduate thesis, or some other substantial document that constitutes scientific writing.


Bugs on alfalfa: A citizen science project to help understand biodiversity


We have launched a citizen science program connected to our funded Dimensions of Biodiversity project aimed at documenting the interactions of various insects with alfalfa plants. Alfalfa (Medicago sativa) is a crop plant introduced to North America in the mid-1800s. It is planted throughout the western US, and has also escaped in many places giving rise to feral populations. We are interested in looking at the arthropod biodiversity supported by both cultivated and feral alfalfa. This provides a powerful opportunity to examine how a non-native plant affects community composition, alters biodiversity, and provides an impetus for the evolution of novel interactions between species.

You can learn more about this project by following the links below:

Article in the Logan Herald Journal

Utah Public Radio interview

USU press release

NSF CAREER award to study fluctuating selection


Thanks to my recent NSF CAREER award, we now have the opportunity to study the ecological causes and evolutionary genomic consequences of spatially and temporally fluctuating selection in Lycaeides butterflies (pictured above). We will use computer simulations, experiments, and genome sequencing of butterflies to understand fluctuating selection, with a focus on how variation in precipitation, temperature, and other factors causes selection on caterpillars to change across space and time. By taking advantage of ~8000 butterfly samples we have collected over the past 30 years and older specimens from museums, we will generate an awesome spatial and temporal population genomic data set that will provide unprecedented insights into contemporary evolutionary change in nature. We even have a new “ancient DNA” room for working with the museum specimens. I will be recruiting a post doc and students to work with me on this project starting in fall 2020.

You can read more about this award in this press release.


Sam’s (PhD student) paper on predictability of genomic change named student authored paper of the year in Molecular Ecology

Sam’s Molecular Ecology paper quantifying the predictability of genomic changes associated with colonization of a novel host plant (alfalfa) by the Melissa Blue butterfly (Lycaeides melissa) was awarded the 2019 Harry Smith prize. This prize is awarded to the best paper published in Molecular Ecology in the previous year by graduate students or early career scholars with no more than five years of postdoctoral or fellowship experience. Congratulations to Sam, this is an awesome achievement!

Science Unwrapped: visualizing arthropod biodiversity on a non-native plant


At USU’s Science Unwrapped public science outreach event in November, Lauren Lucas (pictured above) engaged budding science enthusiast of all ages by allowing them to explore the diversity of arthropods found on alfalfa, an introduced crop plant that has established feral populations across the western USA. This is linked to our own NSF Dimensions of Biodiversity project on the evolution of novel ecological interactions between this introduced plant and arthropods (especially the butterfly Lycaeides melissa) and microbes. Participants were encouraged to classify arthropods based on color (see below) as a way to visualize diversity in a manner accessible to non-specialists.