Research interests

Our research is focused on three main areas:

1. The genetic basis of local adaptation

2. The role of genetic drift in limiting adaptation, and increased risk of extinction

3. The maintenance of outcrossing in predominantly selfing species

We have worked on a variety of plant species, and use a combination of traditional crossing designs, field and greenhouse experiments, and molecular genetic approaches.

1. The genetic basis of local adaptation.

A major goal of evolutionary biology is to understand the factors contributing to the origin and maintenance of biological diversity. Genetic tradeoffs, where adaptation to one environment comes at a fitness cost in an alternate environment, are an intuitive explanation for the ubiquity of adaptive diversification. My research addresses this fundamental hypothesis by investigating the genetic basis of local adaptation and adaptive traits, particularly those that result in fitness trade-offs across environments.

Despite the importance of understanding of the genetic basis of adaptation and fitness tradeoffs, relatively few studies have mapped the genetic basis of fitness, and underlying adaptive traits using reciprocally adapted populations. To better understand the genetic basis of local adaptation and fitness tradeoffs, I combine genetic and genomic tools available in the model plant Arabidopsis thaliana with field and growth chamber studies using genotypes from intact natural populations. This work is part of a collaboration with Jon Ågren (Uppsala University). A multi-year reciprocal transplant study between populations near the northern (Sweden) and southern (Italy) edge of the native range demonstrating strong local adaptation forms the foundation for this work.

We have used a large recombinant inbred line (RIL) mapping population to identify quantitative trait loci (QTL) for fitness in the native sites for eight years. One key result from the first three years of data (Ågren et al. 2013) was that genetic tradeoffs, QTL where the local allele had higher fitness in both environments, are quite common. I subsequently identified large effect QTL for freezing tolerance (Oakley et al. 2014) that colocalize with genetic tradeoff QTL, suggesting that freezing tolerance is the mechanism of some genetic tradeoffs. Freezing tolerance requires a period of cold acclimation (cold but non-freezing conditions) and is therefore an example of adaptive phenotypic plasticity in Sweden. Plants experience cold acclimation conditions in Italy without a subsequent freezing event, and may thus experience a fitness cost of acclimated (induced) freezing tolerance. The casual gene (CBF2) for the largest effect freezing tolerance QTL has been identified and functionally validated (Gehan et al. 2015). Currently we are using CRISPR mutants to examine the effect of sequence polymorphism at CBF2 on global gene expression and metabolite production in response to cold acclimation, and how this relates to freezing tolerance in Sweden, and to fitness tradeoffs across environment (with Brian Dilkes, Purdue).

At the same time, we are using fine mapping approaches with near isogenic lines to identify the causal genes at the other freezing tolerance QTL. We are also addressing questions about parallel evolution by examining the genetic basis of freezing tolerance across different latitudinal and elevational gradients.

2. The role of genetic drift in limiting adaptation, and increased risk of extinction

Most new mutations are somewhat deleterious and partially recessive. In natural populations, random genetic drift reduces the effectiveness of natural selection, leading to high frequency of some deleterious recessive alleles. I have investigated the relative importance of genetic drift in shaping patterns of adaptive genetic variation in nature by estimating heterosis, the increased fitness of an F1 cross relative to the mean fitness of the parents. I remain interested in applications of this approach to conservation biology.

Currently, we are studying the genetic basis of heterosis using F1 crosses from our mapping population of A. thaliana. Using the F1 and both parental lines, and a genome-wide panel of heterozygous NILs, we will estimate heterosis for fitness in growth chambers that simulate both parental environments. The NILs will allow us to partition overall heterosis into the effects of individual genomic regions. Using multiple environments will allow us to additionally study genotype-by-environment interactions for heterosis.

3. The maintenance of outcrossing in predominantly selfing species

Plant mating systems (outcrossing vs. selfing) are important determinants of how adaptive genetic variation is partitioned within and among populations. Theory predicts that complete selfing should evolve unless inbreeding depression is strong enough to favor complete outcrossing. However, many plant species exhibit mixed selfing and outcrossing (mixed mating), and a general explanation of what maintains mixed mating remains elusive. For some time, I have been interested in the maintenance of outcrossing in cleistogamous species. Cleistogamy is a floral heteromorphism that has evolved independently multiple times in many plant families and is characterized by the production of both open (CH), potentially outcrossing flowers, and closed (CL), highly reduced and obligately selfing flowers. In reviewing the literature, I found that reproduction via CL flowers provides a large energetic advantage, and that inbreeding depression in cleistogamous species is generally very low. Therefore, cleistogamy is a compelling case of adaptive mixed mating for which the adaptive significance of outcrossing remains a mystery.

In collaboration with Erin Tripp (UC Boulder), we are investigating the genetic basis of CH/CL in the genus Ruellia, one of the few groups containing cleistogamous species that has a well resolved phylogeny. Cleistogamy has evolved multiple times in Ruellia and occurs in three distinct clades, thus providing an opportunity to study the genetic basis of CH/CL in replicate pairs of sister taxa. This project is in the very early stages, but we hope to have something to report soon.

4. Other projects

We are also begining to investigate freezing tolerance, and tradeoffs between abiotic stress tolerance, pathogen resistance, and yeild in winter wheat in collaboration with Mohsen Mohammadi in the Agronomy Department at Purdue.