Research Projects

All seed plants, some ferns, and some lycophytes, are heterosporous. They produce small dispersing male spores and large, usually static, female spores. The remaining plants are homosporous, producing only one type of spore. Over 50 years ago, researchers noted that homosporous plants have many more chromosomes that heterosporous ones. Chromosome number usually increases through the process of genome doubling (polyploidy). After decades of theory and studies we still do not have a satisfactory explanation for how the condition of spore types can be related to chromosome number. This synthesis brings together ideas and data that have accumulated over 30+ years from my lab, and from others. Using available databases, we are exploring traits that correlate with spore type. We are also looking at gene presence and expression patterns in the genomes of representative homosporous and heterosporous plants. Others involved in this project include Sylvia Kinosian, Pam Soltis, Doug Soltis, Blaine Marchant, and Jim Leebens-Mack.

Since the 1980s, the aquatic fern Ceratopteris richardii has been used as a model organism for genetic and developmental studies. Recently, a draft whole genome for the species was completed. While there has been a great deal of research done on C. richardii, our knowledge of the other species in the genus remains depauperate. Systematists have described the genus as having from one to over half a dozen species and varieties. Considerable morphological variation exists within described species as well as speculated hybridization between species. Due to its increasing use as a model system, a solid taxonomic and systematics understanding of the group is critical. In this study, we begin to unravel the complexity of the species relationships between the species of Ceratopteris. We used double digest restriction-site associated DNA sequencing on 60 samples, representing all currently recognized species, collected from herbarium specimens from around the world. We are exploring polyploidy, hybridization, and genetic relationships. This work is led by Sylvia Kinosian as part of her PhD research.

The typical fern lifecycle consists of two alternating generations – a diploid sporophyte generation that produces spores by meiosis, and a haploid gametophyte generation that produces gametes that fuse to form a zygote through fertilization. Deviations from this “typical” life cycle are fairly common and include forms of asexual reproduction which allow one generation to postpone or avoid transition. Differences in ecological or environmental tolerance of generations have been found, and these differences, combined with long distance spore dispersal, can lead to spores germinating in locations that are not suitable for sporophytes. If the locations are suitable for gametophytes and they reproduce asexually, independent gametophyte populations can be established. The two most well-known fern species with independent gametophyte populations in North America are Trichomanes intricatum and Vittaria appalachiana. The highly reduced plants live in dark, humid, temperature moderated microhabitats on rock outcroppings throughout eastern North America. We are interested in using the distribution of genetic variation within and among populations to better understand their origins and evolutionary history. In addition, since there is evidence that the populations of these two species have existed without sexual reproduction for differing lengths of time, we hope to use them to test expectations of the long-term genetic effects of obligate asexuality. This is part of the dissertation work of Aaron Duffy.

Recently published in American Journal of Botany. Seed‐free plants, including ferns and lycophytes, disperse via spores capable of traveling long distances in air currents. Does this mean that spore‐bearing species are genetically uniform across vast geographic distances? We tested this with one of the most widely distributed plant genera, Pteridium (bracken), a group of ferns with ecological and economic importance. Using over 2800 genetic loci, we compared plants from 100 locations worldwide, and found distinct genetic signatures at the continental scale. “Northern” and “Southern” hemispheres separate two diploid species, and two allotetraploids. We also found several hybrids, especially involving African genotypes, which may produce spores more readily than plants from other areas (due to a drier climate). The results illustrate that despite high dispersal ability and evidence of hybrids across continents, it is still possible to maintain distinct genetic identities on a continental scale.

Ferns represent a major clade of plants for which there was, until very recently, no genome sequence available. For several years, our lab has been exploring genome space in several groups of ferns. This work is in collaboration with former student Josh Der, Kathleen Pryer and Fay-Wei Li, Blaine Marchant, Emily Sessa, Pam Soltis, Doug Soltis. We recently published genome sequences for two heterosporous ferns (link) and working on the much larger genome of the homosporous fern Ceratopteris.