As evolutionary ecologists, we study how organism-environment interactions drive patterns of biodiversity across scales, from alleles and genes to species and communities.

Understanding the processes that generate and maintain natural variation is a fundamental goal in biology, and also a practical concern: evolutionarily, variation is the raw material for adaptive change, and ecologically, the composition and diversity of communities influences ecosystem structure and function. As such, variation both within and among species has consequences for the health and resilience of natural systems.

With a focus on plants and organisms they interact with closely (herbivores, microbes, pollinators, and other plants), our research seeks to answer the following questions:

- How does natural selection shape intraspecific genetic and phenotypic variation?
- What are the consequences of intraspecific variation for species interactions?
- How are these processes linked across scales of biological organization?

We employ multiple methods to answer these questions, including manipulative experiments in the field and greenhouse, molecular techniques in the wet lab, observational field studies, demographic modeling, and quantitative and evolutionary genetics approaches. For more information on specific research projects within these broad themes, see project details below.

study systems

Most of our work employs one of two emerging model systems in plant evolutionary ecology: Boechera (Brassicaceae; left) and Clarkia (Onagraceae; right).

With so many wonderful plants to choose from, why do we study these? Species in both focal genera are relatively small and short-lived, genetically tractable, and amenable to research in both field conditions and controlled greenhouse or growth chamber settings. Both taxa have also been the subject of extensive prior research, which means we know a lot already about the ecology and evolution of these systems, and can build upon that existing knowledge with our ongoing research.

These study systems also take us to beautiful and interesting parts of the world for our fieldwork. Boechera is common in the Rocky Mountains and other parts of the western US, so fieldwork in this genus has taken place in the mountains of Colorado, Idaho, Montana, and more. Most ongoing field projects focusing on Boechera stricta are based out of the Rocky Mountain Biological Laboratory. Most Clarkias, on the other hand, are endemic to California, and current field projects focusing on Clarkia xantiana are based out of the southern Sierra Nevada foothills. We love traveling to our field sites when we can!

If you are are joining the lab, it is likely that your research will focus on one of these taxa. However, the research questions you focus on, and methods you employ to answer them, may vary depending on your interests.

project details

natural selection and polymorphism

Population genetics theory predicts that both directional and stabilizing selection should reduce genetic variation over time, and these forms of natural selection are common. However, genetic variation in adaptive traits persists. Why we continue to observe diverse ranges of phenotypes in natural populations, rather than solely optimal traits, is thus a central question in evolutionary biology.

Using plant secondary chemistry as a focal polymorphism, much of my research has focused on understanding how ecological interactions maintain genetic and phenotypic diversity via balancing selection. Combining field experiments, greenhouse manipulations, molecular analyses, and genetic tools, I have characterized how interactions between biotic and abiotic drivers of selection interact to shape natural variation in leaf chemical profile (Carley et al. 2021) in Boechera stricta, a wild relative of Arabidopsis.

Future research on this topic will explore how changing abiotic conditions, like exacerbated drought under climate change, modulates herbivory and, consequently, variation in plant anti-herbivore defense strategies.

Related miscellany:

- Past work in collaboration with Jill Anderson and RMBL research students has also investigated factors that maintain phenotypic variation in floral color in Boechera stricta (Vaidya et al. 2019).
- While most of my research focuses on natural populations, I am also interested in how human impacts modify these patterns and processes. For example, in in a tropical agroecosystem, I explored how variation in the chemical environment may alter patterns of plant defense expression (Carley & Letcher 2021).

Leaf chemical profile, or “BC-ratio” (the proportion of total glucosinolates derived from branched-chain amino acid precursors), is highly polymorphic across the species range of Boechera stricta.

In the rare species Bochera fecunda (right), standing genetic variation (here, observed heterozygosity) is weakly positively correlated with long-term population growth rates, but variation in inbreeding levels across populations (FIS) is not.

genetic and geographic variation in population dynamics

I am interested in the consequences of intraspecific genetic and phenotypic variation for higher-order processes like local adaptation and population dynamics. Combining long-term demographic data with genetic surveys, I have tested for relationships between genetic variation and extinction risk in a rare species of Boechera endemic to Montana (Carley et al. 2022).

Ongoing work in collaboration with Dave Moeller, Monica Geber and others characterizes long-term population dynamics in Clarkia xantiana, and investigates relationships between demography and adaptation.

Future work on these topics may include:

- Using resurrection studies to estimate evolutionary change in populations that have been monitored over long periods of time, and incorporating this change into demographic models.
- Using genomic sequencing of long-term and historical seed collections to investigate genomic signatures of adaptation and elucidate environmental drivers of selection and population performance.

intraspecific variation in species interactions

Although species exhibit substantial intraspecific genetic and phenotypic variation, the effects of this intraspecific variation on the outcomes of competitive and facilitative interspecies interactions have only recently begun to be incorporated into ecological frameworks. Thus, the extent to which intraspecific variation alters predictions about species coexistence and community composition remains unclear.

Using large-scale field experiments, my work has shown that intraspecific genetic variation can influence the magnitude and direction of plant-plant interactions. Furthermore, the extent to which genetic variation influences plant-plant interactions depends strongly on abiotic contexts.

Future work on this topic will use modeling and empirical approaches to investigate:

- whether and at what spatial scales genetic variation for competition and facilitation might influence coexistence outcomes
- the genetic architecture of intraspecific variation in neighbor interactions
- the evolution of species interactions during diversification and speciation

Effects of heterospecific neighbors on B. stricta. Points represent coefficient estimates regressing (A) growth and (B) reproduction upon neighbor density for each tested accession. The red lines mark 0, with positive effects of neighbors to the right, and negative effects to the left.

Harvesting rhizosphere soil for to characterize microbial community composition.

trait-mediated microbial community assembly

In Brassicaceous plants, there is abundant evidence documenting how variation in glucosinolates influences interactions with herbivores. In addition, recent advances show that these chemicals mediate abiotic interactions like drought tolerance. Simultaneously, these compounds are transported to and exuded through plant roots, with potential effects on interactions between host plants and soil microbes.

Ongoing work using controlled growth chamber experiments investigates how variation in root chemistry influences the diversity and composition of microbial communities in the rhizosphere. Specifically, I aim to understand the extent to which plant genotype and phenotype control microbial community assembly, and whether any such control may feed back to benefit (or harm) plant fitness. This project draws upon experience in microbial bioinformatics that I built through an interdisciplinary collaborative training program (Carley et al. 2020).

Future work in this realm will explore:

- How microbially-controlled fitness differences interact with drought and herbivory to jointly shape glucosinolate evolution and phenotypic diversity
- Whether and how microbial community assembly indirectly contributes to plant drought tolerance
- Potential parallels in belowground effects of glucosinolate exudation across native and non-native taxa in the Brassicaceae

critical perspectives on biological variation

While pursuing the “core” research topics described above, I have become increasingly curious about how history and social contexts influence the frameworks and questions that shape contemporary biological research. In collaboration with Anita Simha and Carlos Pardo de la Hoz, we have developed formal scholarship on this topic using coexistence in ecological communities as a case study (Simha et al. 2022).

In the future, I am interested in pursuing more interdisciplinary work that merges scientific research with critical science studies perspectives and methods. I am also interested in working to operationalize such approaches and explore how changes in conceptual and theoretical frameworks, and the questions and hypotheses they generate, alter inference and interpretation of research outcomes.

Literature review reveals that competition (orange line) has received approximately an order of magnitude more attention in research than have positive or neutral interspecies interactions (purple lines).