Department of Biology

My lab is broadly interested in evolutionary and phylogenetic questions in vascular plants, particularly in the homosporous ferns.

Genome Structure and Evolution in Homosporous Ferns — Homosporous ferns are characterized by high chromosome numbers (n average = 57), suggesting that they are polyploids compared to the heterosporous angiosperms (n average = 16), but isozyme gene expression patterns of ferns are the same as those typical of diploid angiosperms. This paradoxical combination of high chromosome numbers and diploid gene expression led to the hypothesis that homosporous ferns are products of ancient polyploidization events (paleopolyploids) with subsequent divergence and silencing of genes in the extra genomes. With support from the National Science Foundation, we have generated and genotyped ~500 doubled haploid lines (DHLs) to construct a high resolution genetic linkage map of Ceratopteris richardii (right), a model homosporous fern, to investigate this hypothesis. In this first characterization of a homosporous fern genome, we use restriction fragment length polymorphism (RFLP) markers to infer the number of gene copies and their distribution in the genome and amplified fragment length polymorphisms (AFLPs) and isozyme markers to increase saturation of the linkage map. This project is focused on the following questions. Are the majority of genes duplicated? If so, what is the average number of copies for each gene? Do most genes have a similar number of copies, or do they vary widely in copy number? How are duplicate genes distributed across the genome? Are entire sets of genes duplicated and recognizable as homoeologous chromosomal segments, or are paralogues scattered haphazardly across the genome? If paleopolyploidization is evident, are homoeologous chromosomes recognizable or are they highly rearranged? Duplication of all or most sets of genes combined with collinear gene orders for duplicated chromosomal segments would provide strong evidence of past polyploidization. Resulting publications that answer some of these questions to date are those from 2006 and 2007 in the listing below.

Homosporous ferns are the vast majority of species that compose the clade that is the phylogenetic sister group to seed plants. Our high resolution genetic linkage map of a model homosporous fern is therefore significant for the following reasons. 1) It provides the first detailed characterization of a genome of a homosporous vascular plant, thereby broadening our knowledge of the evolution of genome structure in vascular plants. 2) It generates the most comprehensive evidence bearing on paleopolyploidy in homosporous ferns to date, thus providing the foundation for future studies of their biology and evolution. 3) It makes available to the scientific community the ~500 fully genotyped DHLs of plants developed in the course of this genome mapping project.

Molecular Phylogenetics and Systematics of Desert-Adapted Cheilanthoid Ferns — Specialists consider cheilanthoid ferns as one of six subfamilies of the homosporous fern family Pteridaceae and have long regarded them as a major evolutionary unit of several hundred species largely adapted to xerically harsh, semi-desert conditions, as in the southwestern U.S. and Mexico. These same specialists have also conceded that determining natural evolutionary lines within this group by traditional taxonomic means is virtually impossible, perhaps because convergent evolution has strongly modified the morphological features of cheilanthoid species as they became adapted to their harsh environments, as exemplified (right) by this species of Cheilanthes growing among boulders in a Nevada habitat that becomes seasonally very hot and dry. We use cladistic analysis of phylogenetically informative molecular data (mutations in chloroplast DNA restriction sites and in the nucleotide sequences of chloroplast and nuclear genes) to infer major evolutionary lineages that can be recognized as natural genera and infrageneric taxa within the cheilanthoid ferns.