Category Archives: Uncategorized

New paper in Science Advances shows we can predict host plant use by the butterfly Lycaeides melissa

The first big paper from our NSF Dimensions of Biodiversity project is now out at Science Advances. To better understand the recent adoption of alfalfa as a host plant by the Melissa blue butterfly (Lycaeides melissa), we quantified arthropod assemblages and plant metabolites across a wide geographic region while controlling for climate and dispersal inferred from population genomic variation.

Map of study locations, dispersal surface, and images of butterflies, ants and caterpillar.

We found that the presence of L. melissa could be reliably predicted by direct and indirect effects of plant traits and interactions with other species. The single biggest factor was the presence versus absence of ants, which tend Lycaeides caterpillars, thereby reducing attacks by predators. Our results suggest that host use and specialization arises as a consequences of many abiotic and biotic factors rather than from simple trade-offs in developmental physiology.

New postdoc and PhD student

We are excited to welcome two new lab members this fall.

Linyi Zhang is a new postdoc in the lab. She completed her PhD with Scott Egan at Rice. She is broadly interested in adaptation and speciation, and her past work focused on how divergent host use promotes reproductive isolation among sympatric populations of gall wasps. She is currently combing genome-wide association mapping and whole genome sequencing of natural butterfly populations to determine the causes and consequences of (potentially) fluctuating selection on polygenic traits.

Brian Kissmer began his PhD in the lab this fall. He is interested how the nature and repeatability of adaptation depends on the degree to which a population is maladapted to a novel environment. He is initially addressing this question using experimental evolution in Callosobruchus maculatus seed beetles.

Non-linear selection on color causes fitness epistasis in a field experiment, new paper out in Nature E&E

Theory indicates that non-linear selection (e.g., stabilizing, disruptive, or correlational selection) on traits can result in epsitasis for fitness even when alleles have additive affects on traits. In a paper recently published in Nature Ecology and Evolution, we demonstrate this in a field experiment with Timema stick insects. In particular, we show that color is determined mostly by alleles with additive effects, but that selection for crypsis favors color combinations resulting in epistasis for fitness. This in turn results in a rugged fitness landscape with respect to the color loci.

See our blog post for more thoughts and background on the paper.

Supermutation and the evolution of discrete color morphs in stick insects


Timema petita (photo by R. Villoutreix)

In a new paper in Science we show how a large-scale (1 million base pair) deletion converts a continuum of body colors into discrete color morhps, and thereby likely increases crypsis in Timema stick insects. This deletion is also the breakpoint of an inversion, and thus our work shows that inversions can affect evolution in ways other than by suppressing recombination, that is by directly causing major mutations. More generally, this paper demonstrates a way that gene complexes can be packaged into (semi) discrete units of diversity, which has implications for understanding the evolution of other units such as sexes and species.

You can read more about the paper on EurkaAlert and the EcoEvo blog.

Completing specition, new paper and special issue

Arguably, research in speciation has focused more on how the process begins, that is, how the first barriers evolve, than on the later stages of the speciation process (i.e., the evolution of [nearly] complete reproductive isolation). A recent special issue in Philosophical Transactions of the Royal Society B seeks to partially rectify this issue. We analyze this issue in the context of host shifts in Timema stick insects. In particular, in an article in this special issue we show that host shifts to closely related plant species are common, but cause only weak reproductive isolation. In contrast, much rarer host shifts from flowering plants to gymnosperms generate strong reproductive isolation. Thus, such rare and difficult events might be important for generating fully isolated species.hostpic

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.