Research Interests

The research of the Lowry lab is centered on identifying the genetic and genomic mechanisms of ecological adaptations and how those adaptations contribute to the formation of new species. To understand the physiological, developmental, and genetic mechanisms of adaptive divergence between plant populations, the Lowry lab is focused on research in three flagship systems for evolutionary genomics: Monkeyflowers (Mimulus), Common Bean (Phaseolus), and Panicum grasses. Large communities of collaborative scientists have established extensive genomic and molecular biology resources for these systems.

How does natural selection contribute to the process of speciation?

The process of speciation occurs as a continuum over time, and involves multiple stages from divergent populations to distinct phylogenetic lineages. Natural selection often plays a primary role in the early stages of speciation through the formation of ecotypes. However, there is still much to learn about how natural selection drives the evolution of reproductive isolation. The contributions of individual environmental factors to reproductive isolation have yet to be quantified for any system, the physiological mechanisms involved in the early stages of speciation have only rarely been identified, and we still have a limited understanding of how individual genetic loci contribute to ecological reproductive isolation. Through previous research, Lowry has identified several environmental factors involved in reproductive isolation, developed methods for quantification of the contribution of individual loci to reproductive isolating barriers, and established a framework for studying stages in the process of speciation. IMG_5464

One of the key mechanisms by which ecotypes are thought to evolve into divergent species is through the evolution of ecogeographic reproductive isolation. Ecogeographic isolation restricts gene flow by maintaining an allopatric distribution between diverging ecotypes as a result of local adaptation to divergent habitats. Since ecogeographic isolation causes an allopatric distribution of ecotypes, it will promote the accumulation of adaptive and neutral genetic differences that can contribute to the evolution of other reproductive isolating barriers over time. Therefore, establishing the causes of the adaptive fitness trade-offs that promote ecogeographic isolation is a crucial step toward understanding the process of speciation.

The Lowry lab is currently working to address the following fundamental questions regarding the evolution of ecogeographically isolated ecotypes: 1) How do different environmental factors (drought, herbivory, and competition) contribute to the fitness trade-offs that are responsible for ecogeographic reproductive isolation? 2) Which genetic and physiological mechanisms cause the divergence in growth form of ecotypes that is responsible for fitness trade-offs? 3) Do gene expression responses mirror the overall patterns of fitness trade-offs across the habitats that drive ecogeographic reproductive isolation? These questions will be answered in the Mimulus guttatus system using a combination field, laboratory, and genomic methods.

What are the mechanisms of adaptation along environmental gradients?
IMG_2709
We are also very interested in how individual loci contribute to local adaptation across large environmental gradients. To understand the role of individual loci across a broad latitudinal gradient, we are studying the bioenergy crop switchgrass (Panicum virgatum). Switchgrass populations are adapted to local climatic conditions across the Great Plains of North America through the evolution of flowering time, pathogen resistance, drought tolerance, and cold tolerance. Since 2010, Lowry has been working to develop a genetic mapping population derived from a cross between two northern and two southern clones of switchgrass. In 2015, we planted this mapping population at 10 locations from South Texas to the northern Great Plains. In the coming years, we will use these common gardens to identify genomic regions involved in adaptation to the latitudinal gradient of natural selection that exists across the Great Plains of North America. We will be particularly interested in conducting quantitative trait locus (QTL) mapping to identify the regions of the genome that control crucial biofuel traits like tissue digestibility, drought tolerance, and pathogen resistance.

How do chromosomal rearrangements contribute to adaptation and speciation?

IMG_8906One of the major ongoing projects in the Lowry Lab is a quest to understand the mechanisms by which chromosomal inversions contribute to adaptation and reproductive isolation. Chromosomal inversions are very important for human health, as they underlie many genetic diseases and affect the geographic distribution of mosquitoes that vectors malaria. Inversions have long been thought to be involved in ecological adaptations, ever since pioneering cytogenetic analyses in Drosophila revealed that inversion polymorphisms track environmental gradients. Inversions also suppress meiotic recombination. One of the consequences of suppressed recombination is that alleles at linked loci within inversions will be maintained as distinct haplotypes. As a result, researchers have long suspected that inversions operate as adaptation “supergenes” by maintaining functional allelic divergence at multiple linked loci through suppressed recombination. Numerous studies have connected inversions to adaptation and increasing evidence suggests that inversions may act as supergenes, but definitive results are lacking.

During graduate school, Lowry discovered a chromosomal inversion polymorphism that is involved in adaptive divergence and reproductive isolation between coastal perennial and inland annual ecotypes of Mimulus guttatus in western North America. The inversion contributes to major changes in the overall phenotype of the plants as well as to local adaptation in nature. We are now working to determine the evolutionary, molecular genetic, and physiological mechanisms by which the inversion has contributed to this important evolutionary transition. To accomplish that goal, we are on taking multiple approaches, including pooled genome sequencing, gene expression analyses, and analyses of chromatin accessibility. Our goal is to identify adaptive genes within the inversion in order to test whether the inversion is operating as an adaptation supergene.

What are the genetic mechanisms of stress tolerance in common bean?

Common bean is one of the most important food legumes grown worldwide and one of the leading sources of protein in Latin America and sub-Saharan Africa. Bean is also an ideal system for answering basic research questions in adaptation and speciation because it is a self-fertile diploid with a comparatively small genome. Production of bean is limited by drought, heat, and a suite of pathogens. With global climate change, those stresses are likely to become more intense, further hampering the production of common bean worldwide. Innovative approaches to improve germplasm are now needed make common bean more resilient to stress and ensure success across a variety of ecoregions worldwide. Our research on stress tolerance genetics in bean leverages extensive resources available for bean, including large fully genotyped GWAS panels, numerous advance generation hybrid populations, and extensive data sets from field trials across Africa, the Caribbean, and North America. This research is sponsored by the new Plant Resilience Institute at MSU.

What are the genes underlying climatic adaptations?

IMG_6379To identify the genes involved in adaptation to different climates, we are working with the model genomic system, Panicum hallii. P. hallii is closely related to switchgrass, but is much easier to work with due to a short generation time, smaller size, and simpler (diploid) genetics than P. virgatum. We have fully sequenced nearly 100 population accessions of P. hallii from across the southwestern United States in collaboration with the Joint Genome Institute (DOE). We are conducting population genomic analyses with those sequenced accessions to identify regions of the genome involved in adaptation. We are particularly interested in the adaptive divergence of P. hallii populations across the Chihuahuan and Sonoran Deserts. Hot, dry desert valleys that divide “sky island” mountain ranges characterize both of those desert regions. We aim to understand the mechanisms of adaptive divergence between the sky islands and desert valley populations. This research will serve as both a model for the evolution of adaptation to future climate change and as a model for improvement of switchgrass as a bioenergy feedstock.