The complex genomes of Ferns

Ferns (monilophytes) 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. The research is published in Genome Biology and Evolution: link and Applications in Plant Sciences: link. We also recently published genome sequences for two heterosporous fern (link) and working on the much larger genome of the homosporous fern Ceratopteris.

Origins of Galapagos Pteridium

This Study builds on previous work by Josh Der than examined a global chloroplast phylogeny for Pteridium. Here we use this as a launching point to examine origins of Pteridium on the Galapagos Islands. Earlier reports suggest that more than one taxon may be found on the islands. Furthermore, ferns are dispersed by tiny airborne haploids spores. This increases the chances of colonization occurring though fertilization between spores of different sources, leading to hybrids. This contrasts with seed plants which are dispersed through diploid seeds. We are using the same two chloroplast genes from the previous study plus two nuclear genes to examine the origins of Pteridium collected on three of the Galapagos islands: San Cristobal, Isabella, and Santa Cruz. This work is also being expanded for a worldwide study of the genus.

Cytogenetics and population genomics of Aspen (Populus tremuloides)

Aspen (Populus tremuloides) is the most widely distributed tree species in north America. In collaboration with Karen Mock, we are exploring genome-scale variation and the distribution of cytotypes. In some parts of western north America, more than half the aspen individuals are triploid. We are exploring genetic and physiological differences between diploids and triploids. We are also aim to search for candidate loci that may affect local adaptation in aspen using single nucleotide polymorphisms (SNPs). We are using Genotyping by Illumina Sequencing to gather SNP data on aspen. Martin Schilling is working on this project.

Systematics and Conservation Genetics of the Eriogonum corymbosum Complex

The taxonomic placement of buckwheat populations found in and around Las Vegas, NV, has been uncertain. Recently they were given their own varietal designation Eriogonum corymbosum var. nilesii, based on morphological traits. With funding from the US Fish and Wildlife Service and the Nevada Native Plant Society, we are examining these populations to see if there is genetic support for this new taxon. Our data, including AFLPs (Amplified Fragment Length Polymorphisms) of genomic DNA and chloroplast sequences, support the relative uniqueness of these populations. We are also looking at the geographic distribution and phylogenetic relationships of the complex of E. corymbosum varieties and related species in both the Great Basin and Colorado Plateau regions. This is the primary dissertation (and post-dissertation) work of Mark Ellis. Recently, we have explored recently discovered populations of var. nilesii, outside the initial known range. This implies that the taxon may not be as rare or restricted as previously thought.

Evolution of the matK Gene in Ferns

In the seed plants, the matK gene found in the chloroplast genome is often used as a phylogenetic marker. The presence of both highly conserved and highly variable regions makes it potentially useful in studies at a range of taxonomic levels. However, matK has not been used in studies of ferns because the universal primers used in other taxa do not work. In most land plants the matK gene is located within an intron of the trnK gene and is thought to play a role in splicing out the intron. However in the lineage leading to most fern species, a large inversion separated one trnK exon and part of the intron from matK. In the recently completed Adiantum capillus-veneris genome, the trnK gene is no longer present yet the matK sequence is still recognizable, suggesting that matK still has some function. We are interested in using ratios of nonsynonymous and synonymous mutations to look for evidence of differences in selective pressure on the matK sequence in taxa with and without trnK. In addition, we are developing universal primers to amplify and sequence matK in other fern taxa. Aaron Duffy is working on this project.

Breeding Biology and Population Genetics of Maguire Primrose

Maguire primrose is a locally endemic plant of northern Utah, USA, with a total known range of less than 20 km2. A previous study found evidence for strong differentiation among local populations at 4 allozyme loci. We reexamined populations using 165 AFLP loci and found further evidence of unusually strong genetic structure. We also found an apparently fixed nucleotide difference between populations for a noncoding region of chloroplast DNA, mirroring the patterns seen for AFLP loci. Furthermore, we tested the hypothesis that the current population structure is the result of breeding barriers between plants from different populations. We made controlled hand-pollinated crosses and found that interpopulation crosses did not set significantly fewer seeds than intrapopulation crosses. Thus, we found no evidence of breeding barriers to explain these genetic patterns. As part of his masters thesis project, Jacob Davidson examined the breeding system and found that this species is primarily outcrossing and requires an insect pollinator. The most common floral visitors are anthophorid bees. See Jake's paper published in Plant Species Biology here

Independent Gametophyte Populations

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.