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. A key goal of our research is to link adaptive genetic variation with features of the natural landscape. To understand the physiological, developmental, and genetic mechanisms of adaptive divergence between plant populations, the Lowry lab is focused on research in two major emerging model systems for evolutionary genomics: Monkeyflowers (Mimulus) and Panicum grasses, including the bioenergy crop switchgrass. Two large communities of collaborative scientists have established extensive genomic and molecular biology resources for these systems.
The role of chromosomal rearrangements in adaptation and speciation
One of the major ongoing projects in the Lowry Lab is a quest to understand how 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 also 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.
Understanding the mechanisms of adaptation along environmental gradients
The Lowry Lab is very interested in determining the genetic mechanisms of the morphological, physiological, and life-history transitions that accompany adaptation to habitats that differ in soil water availability. The chromosomal inversion, mentioned above, is involved in one such transition. More recently, we have become interested in parallel adaptive transitions of this sort in Panicum grasses. This includes the bioenergy crop switchgrass (Panicum virgatum), which may be used in the future for production of cellulosic ethanol and other biofuels. Switchgrass has both upland and lowland ecotypes that are adapted to dry and wet habitats, respectively. Since 2010, Lowry has been working to develop a genetic mapping population derived from a cross between two northern upland and two southern lowland individuals. 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.
Development of a new model system for climatic adaptation and bioenergy research
The Lowry lab is working on similar questions of adaptation to differences in soil water availability in a new 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.