Study Systems

Brassica: The plants of Brassica are well known as the “dogs” of the plant world because of their morphological diversity. A series of nested polyploid speciation, or whole genome duplication, events occurred in the ancestry of these plants. We are currently studying how polyploidy contributed to the diversity of the Brassica crops (e.g., turnip, Chinese cabbage, canola oil, broccoli, cauliflower, kale, cabbage, etc.). These crops are a model agricultural system for understanding how changes in natural selection and genetic variation following polyploidy may drive diversity.

The famous “Triangle of U” hypothesis of relationships among the diploid and allopolyploid species of Brassica. Originally proposed by Woo Jang-choon. Image from wikipedia.

Selaginella: A local group of lycophytes with some of the smallest plant nuclear genomes (smaller than Arabidopsis!). These plants dessicate during dry periods and resurrect when it is wet again. They can be resurrected from collections, including 100 year old herbarium sheets! We are working on two different local species complexes that contain hybrid and polyploid species. These occur throughout the Sonoran Desert and the Madrean Sky Islands. The Sky Islands create natural barriers to gene flow among populations and provide interesting evolutionary experiments for us to explore. Focal species currently include S. arizonica, S. eremophila and their diploid and polyploid hybrids as well as the allotetraploid S. rupincola. We use these species to study the population genomics of hybridization and polyploidy in plants.

The allotetraploid lycophyte Selaginella rupincola growing among the boulders at Cochise Stronghold in the Dragoon Mountains southeast of Tucson, Arizona. Image credit M. S. Barker.
The diploid Selaginella arizonica resurrecting to the remnants of Hurricane Newton in September 2016. This population is located near Gate’s Pass in Tucson, Arizona. The reference genome for S. arizonica and part of our mapping population were sampled from nearby sites.

Plant Ecological & Evolutionary Genomics with NEON: The ability of an organism to acclimate to different environmental conditions through its lifetime — termed phenotypic plasticity — is one of the primary ways that organisms cope with periods of environmental variation. It has been difficult to test hypotheses about phenotypic plasticity, however, because important plastic changes can be hard to observe. Often, critical biological processes are maintained on the surface by flexible changes in the underlying physiology. Surveys of gene expression (the extent to which a gene is turned on in cells) offer a new way to observe plasticity at the most basic level of function of an organism. This project explores the feasibility of using gene expression to study the plasticity of plants at a broad scale, and tests the specific hypothesis that two types of plants are especially adept at utilizing phenotypic plasticity: invasive species and species with duplicated copies of their genomes (i.e., polyploids). The NEON network provides an exceptional platform across which the plastic responses of these different categories of species to environmental variation can be compared. This study will leverage NEON’s long-term study sites and data on plant species abundance to determine how plasticity at the level of gene expression may predict which plants will be most successful in a community. A major goal of this project is to establish a method by which plant performance can be tracked over time and space in the NEON network, to aid humanity in anticipating the decline, stability, and spread of native and invasive species.

Our first analyses supported by a NSF EAGER-NEON award are currently underway at Harvard Forest. Sets of related diploid, polyploid, and invasive species were collected from two time points this past summer with additional collections planned for next year.

Dr. Hannah Marx and PhD student Stacy Jorgensen collecting tissue in July 2016 for RNA isolation at Harvard Forest, our pilot study site in the NEON network. Image credit to H. Marx.
The equipment needed to sample the genetic diversity of a forest. Image credit H. Marx.

The Hawaiian Silversword Alliance: An outstanding adaptive radiation of more than 35 species of composites on the Hawaiian islands. Following allopolyploid speciation, these species radiated into nearly every habit (vines, trees, shrubs, etc) and life history observed in plants. We are studying how hybridization and genome duplication contributed to this amazing radiation. The Hawaiian Silversword Alliance is an amazing model system for exploring hypotheses of how polyploidy may drive the diversification of plants.


Plants, insects, vertebrates, and everything in between: To better understand the history of polyploidy in the evolution of life on earth we use our bioinformatic tools to document and analyze paleopolyploidy across the tree of life. Numerous public (e.g, 1KP) projects are generating phylogenetically broad genomic data that we analyze. If you have a favorite group of organisms with new genomic data, chances are we would like to analyze them!