Research

Research projects in the lab

concept map2

Most of our research addresses the central question above and focuses on ferns and/or lycophytes, but we also have several projects that are not fern-centric. See below for descriptions of the major active projects in the lab.

Moss - 07GoFlag: Building a comprehensive evolutionary history of flagellate plants

For the first ~300 million years of plant life on land, Earth’s flora consisted entirely of flagellate plants, which today include approximately 30,000 species of bryophytes, lycophytes, ferns, and gymnosperms. Numerous major innovations, including stomata, vascular tissue, roots and leaves, woody stems, and seeds, evolved first in flagellate plant ancestors. The flagellate plants not only provide a window to the early evolution of these critical features, but are represented today by vibrant and diverse lineages that contribute substantially to global ecology, particularly via contributions to global carbon and nitrogen cycles. We are working to improve our understanding of the history and relationships of the flagellate plants by using new sequencing technologies to produce a species-level phylogeny for these taxa that is linked to an immense and varied amount of data on fossils, phenomic characters, and geospatial distributions. Education experts will develop an online educational tool for training the next generation of biodiversity scientists by providing an accessible framework for using the project data in university classrooms while promoting evidence-based teaching practices. A MicroPlants citizen science project will promote scientific literacy and plant awareness in the general public, through museums and schools. This project is a collaboration with the Burleigh, Davis, McDaniel, and Antonenko labs at UF, and at the Field Museum (Matt von Konrat and Eve Gaus) and University of Arizona (Hong Cui).

 

Dryopteris wallichianaAfrican ferns: Phylogenetics and historical biogeography
The continent of Africa contains fewer fern species in general than regions in the neighboring Neotropics and Old World tropics, and very little is known about the relationships of African species to their congeners in other regions. We are working on reconstructing phylogenies for genera that include African species in order to understand how they are related to species in other areas, and to reconstruct their historical biogeography to determine when and from where their ancestors migrated to Africa. We are also examining diversification of African ferns to determine what climatic and other factors might be correlated with their evolution. This work is part of an ongoing collaboration with Aino Juslén, and Henry Väre at the Finnish Museum of Natural History.

Publications:

  • Sessa EB, A Juslén, H Väre, and SM Chambers. (2017) Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris). American Journal of Botany. 104(3): 447–486. PDF

 

IMG_2489Community phylogenetics of Florida ferns & Pine Rocklands
The Sessa lab has several collaborative projects with Ben Baiser of UF’s Department of Wildlife Ecology & Conservation that are focused on community phylogenetics. The state of Florida has the richest fern flora of any state in the continental U.S. It is home to 149 species of ferns, including ~120 that are thought to be native. We are using community phylogenetic methods and niche modeling to explore georeferenced data for these species, in order to examine distributions, diversity, and various components of community structure for all the ferns in Florida. Community phylogenetic methods enable us to examine the dynamics of plant community and ecosystem assembly in the context of species’ evolutionary histories. Combined with ecological, functional, and climatic data, we can take an integrated approach to understanding the various biotic, abiotic, and evolutionary components driving patterns of diversity in communities at different temporal and spatial scales.

The Pine Rockland ecosystem is a globally imperiled system of fragmented habitats in South Florida that are home to 500+ plant species and numerous animal, fungal, and bacterial taxa. In another ongoing collaboration with Ben Baiser (Wildlife Ecology & Conservation, UF), we are working to characterize the plant and herbivore diversity in these communities in order to identify feeding links and construct food web networks for this ecosystem. We are currently building a community phylogeny for all of the plant taxa in these habitats, which will be the starting point for analyses of functional and phylogenetic diversity in Pine Rockland fragments, and for analyzing insect feeding strategies and building food webs. Lauren Trotta, a MS/PhD student in the Baiser and Sessa labs, has constructed this phylogeny and used it to investigate the relationships among invasive, threatened and endangered, and endemic Pine Rockland species in order to inform conservation and management efforts.

 

Version 2Phylogenetics of Dryopteris & Asplenium
The phylogenetic relationships and evolutionary histories of various groups of ferns are a major area of interest in the Sessa lab. Two primary genera that we focus on are Dryopteris (the woodferns), and Asplenium (the rockferns). For Dryopteris, we are working towards constructing a worldwide phylogeny for all 400+ species that will serve as a basis for revising the global classification system for the genus. This is a collaboration with Libing Zhang (Missouri Botanical Garden), Aino Juslén, and Henry Väre (Finnish Museum of Natural History). We are also investigating the history of reticulate evolution in both Dryopteris and Asplenium, focusing on species complexes in North America, Europe, and Africa, in order to assess the relative frequency of recurrent polyploidization and its potential effects on genetic variation and implications for species concepts. Related studies on the North American species have investigated physiological traits and whether there is evidence that North American Dryopteris taxa are adapted specifically to the light environments in which they most commonly occur. In a Mediterranean complex of Asplenium, we are trying to determine whether there is evidence from chloroplast markers for asymmetric hybridization among members of the group. This project is a collaboration with José Maria Gabriel y Galan and his students (Universidad Complutense Madrid).

Publications:

  • Sessa EB, A Juslén, H Väre, and SM Chambers. (2017) Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris). American Journal of Botany. 104(3): 447–486. PDF
  • Sessa EB, L-B Zhang, H Väre, and A Juslén. (2015) What we do (and don’t) know about ferns: Dryopteris as a case study. Systematic Botany 40(2): 387–399. PDF
  • Sessa EB and TJ Givnish. (2014) Leaf form and photosynthetic physiology of Dryopteris species distributed along light gradients in eastern North AmericaFunctional Ecology 28(1): 108-123. PDF
  • Sessa EB, EA Zimmer, and TJ Givnish. (2012) Unraveling reticulate evolution in North American Dryopteris  (Dryopteridaceae). BMC Evolutionary Biology 12(1): 104. PDF
  • Sessa EB, EA Zimmer, and TJ Givnish. (2012) Reticulate evolution on a global scale: a nuclear phylogeny for New World Dryopteris (Dryopteridaceae)Molecular Phylogenetics & Evolution 64(3): 563-581. PDF
  • Zhang L-B, L Zhang, S-Y Dong, EB Sessa, X-F Gao, and A Ebihara. (2012) Molecular circumscription and major evolutionary lineages of the fern genus Dryopteris (Dryopteridaceae). BMC Evolutionary Bio 12(12): 180. PDF
  • Sessa EB, EA Zimmer, and TJ Givnish. (2012) Phylogeny, divergence times, and historical biogeography of New World Dryopteris (Dryopteridaceae). American Journal of Botany 99(4): 730-750. PDF

 

Adiantum pedatum - 09Fern genomics
Sequencing studies have successfully produced reference genomes for almost every major lineage of green plants, including over 100 angiosperm species, enabling great strides in crop improvement as well as evolutionary inference. Surprisingly, no sequenced genomes are available for any member of the fern clade, the second largest vascular plant clade after the angiosperms, and currently the only major vascular plant lineage without a reference nuclear genome sequence. There is also no genome sequence available for any homosporous vascular plant; ferns represent the largest such group. The Sessa lab is involved with efforts to change this. We have also collaborated with  Paul Wolf (Utah State University)Josh Der (California State University, Fullerton)Pam and Doug Soltis (UF) and others to explore genome space in several ferns via genome skimming.

Publications:

  • Sessa EB and JP Der. (2016) Evolutionary genomics of ferns and lycophytes. Pgs. 215–254 in: Genomes and Evolution of Charophytes, Bryophytes, and Ferns. SA Rensing, Ed. Advances in Botanical Research, vol. 78. Elsevier. Request PDF
  • Wolf PG, EB Sessa, DB Marchant, F-W Li, CJ Rothfels, EM Sigel, MA Gitzendanner, CJ Visger, JA Banks, DE Soltis, PS Soltis, KM Pryer, and JP Der. (2015) An exploration into fern genome space. Genome Biology and Evolution 7(9): 2533–2544. PDF
  • Sessa EB, JA Banks, MS Barker, JP Der, AM Duffy, SW Graham, M Hasebe, J Langdale, F-W Li, DB Marchant, KM Pryer, CJ Rothfels, SJ Roux, ML Salmi, EM Sigel, DE Soltis, PS Soltis, DW Stevenson, and PG Wolf. (2014) Between two fern genomes. GigaScience 3:15. PDF

 

IMG_9443Fern mating systems
Homosporous land plants utilize three different mating systems, one of which, intragametophytic selfing, is an extreme form of inbreeding only possible in homosporous groups (which includes the majority of ferns). This mating system results in complete homozygosity in sporophyte progeny and has important evolutionary and ecological implications. Ferns are the largest group of homosporous land plants, and the prevalence of intragametophytic selfing in this lineage has been a subject of debate for decades. We are collaborating with Eddie Watkins (Colgate University) and Weston Testo (Barrington Lab, University of Vermont) to quantify the frequencies of different mating systems in homosporous ferns and examine associations between breeding systems and a variety of ecological and evolutionary traits.

Publications:

  • Haufler CH, KM Pryer, E Schuettpelz, EB Sessa, DR Farrar, R Moran, JJ Schneller, JE Watkins, Jr., and MD Windham. (2016) Sex and the single gametophyte: Revising the homosporous plant life cycle in light of contemporary researchBioScience. In pressPDF.
  • Sessa EB, WL Testo, and JE Watkins, Jr. (2016) On the widespread capacity for, and functional significance of, extreme inbreeding in ferns. New Phytologist 211 (3): 1108–1119PDF

 

1kp projectOne Thousand Plant Transcriptomes (1KP) project
The goal of the 1KP project is to sequence transcriptomes from over 1000 species of plants. The Sessa lab is contributing samples for sub-projects on fern phylogenomics and comparative transcriptomics between gametophytes and sporophytes across land plants. When we consider land plants as a whole, several of the most striking differences between the major lineages include dramatic changes in relative size, function, and duration of the gametophyte and sporophyte stages of the life cycle. Across land plants, there is a transition from a dominant gametophyte with dependent sporophyte in the bryophytes, to independent gametophytes and dominant sporophytes in the lycophytes and ferns, to a highly reduced, ephemeral, and dependent gametophyte in the seed plants, particularly in angiosperms. This life history transition is accompanied by numerous innovations in both sporophyte and gametophyte morphology and ecology. We will use data produced by the 1KP project to investigate changes in gene expression patterns in both life stages across land plants. This work is a collaboration with Sean Graham (UBC), Josh Der (California State University, Fullerton), Dennis Stevenson (NYBG), and many others.

 

goodeniaceaePhylogenetics of Goodeniaceae
We are collaborating with a research team led by Rachel Jabaily (Rhodes College) to produce a phylogeny for the Australian fan-flower family, Goodeniaceae. Goodeniaceae is sister to the major angiosperm clade Asteraceae plus Calyceraceae, and includes 420+ species that are primarily endemic to Australia, with multiple radiations of the genus Scaevola in Pacific island systems. We are using a genome skimming approach to generate plastid and nuclear sequence data that will be used to reconstruct the backbone phylogeny of this group, in order to determine the relationships between major, well-supported clades. This phylogeny will form the basis for studies of floral evolution, including gene expression studies overseen by Dianella Howarth (St. John’s University). Photos of Goodenia taxa above by Andy Gardner, postdoc in the Jabaily lab.

Publications:

  • Gardner AG*, EB Sessa*, P Michener, E Johnson, KA Shepherd, DG Howarth, and RS Jabaily. (2016) Utilizing next-generation sequencing to resolve the backbone and inform taxonomy of the Core Goodeniaceae. Molecular Phylogenetics and Evolution 94: 605–617. PDF *These authors contributed equally.