Paul G. Wolf

A classification for extant ferns

We present a revised classification for extant ferns, with emphasis on ordinal and familial ranks, and a synopsis of included genera. Our classification reflects recently published phylogenetic hypotheses based on both morphological and molecular data. Within our new classification, we recognize four monophyletic classes, 11 monophyletic orders, and 37 families, 32 of which are strongly supported as monophyletic. One new family, Cibotiaceae Korall, is described. The phylogenetic affinities of a few genera in the order Polypodiales are unclear and their familial placements are therefore tentative. Alphabetical lists of accepted genera (including common synonyms), families, orders, and taxa of higher rank are provided.

Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants

Most of the 470-million-year history of plants on land belongs to bryophytes, pteridophytes and gymnosperms, which eventually yielded to the ecological dominance by angiosperms 90 Myr ago. Our knowledge of angiosperm phylogeny, particularly the branching order of the earliest lineages, has recently been increased by the concurrence of multigene sequence analyses. However, reconstructing relationships for all the main lineages of vascular plants that diverged since the Devonian period has remained a challenge. Here we report phylogenetic analyses of combined data—from morphology and from four genes—for 35 representatives from all the main lineages of land plants. We show that there are three monophyletic groups of extant vascular plants: (1) lycophytes, (2) seed plants and (3) a clade including equisetophytes (horsetails), psilotophytes (whisk ferns) and all eusporangiate and leptosporangiate ferns. Our maximum-likelihood analysis shows unambiguously that horsetails and ferns together are the closest relatives to seed plants. This refutes the prevailing view that horsetails and ferns are transitional evolutionary grades between bryophytes and seed plants, and has important implications for our understanding of the development and evolution of plants.

A community-derived classification for extant lycophytes and ferns

Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community‐based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.

De novo Characterization of the Gametophyte Transcriptome in Bracken Fern, Pteridium Aquilinum

BackgroundBecause of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in ferns combined with the absence of economically important species have been a barrier to the development of genomic resources. However, high throughput sequencing technologies are now being widely applied to non-model species. We leveraged the Roche 454 GS-FLX Titanium pyrosequencing platform in sequencing the gametophyte transcriptome of bracken fern (Pteridium aquilinum) to develop genomic resources for evolutionary studies.Results681,722 quality and adapter trimmed reads totaling 254 Mbp were assembled de novo into 56,256 unique sequences (i.e. unigenes) with a mean length of 547.2 bp and a total assembly size of 30.8 Mbp with an average read-depth coverage of 7.0×. We estimate that 87% of the complete transcriptome has been sequenced and that all transcripts have been tagged. 61.8% of the unigenes had blastx hits in the NCBI nr protein database, representing 22,596 unique best hits. The longest open reading frame in 52.2% of the unigenes had positive domain matches in InterProScan searches. We assigned 46.2% of the unigenes with a GO functional annotation and 16.0% with an enzyme code annotation. Enzyme codes were used to retrieve and color KEGG pathway maps. A comparative genomics approach revealed a substantial proportion of genes expressed in bracken gametophytes to be shared across the genomes of Arabidopsis, Selaginella and Physcomitrella, and identified a substantial number of potentially novel fern genes. By comparing the list of Arabidopsis genes identified by blast with a list of gametophyte-specific Arabidopsis genes taken from the literature, we identified a set of potentially conserved gametophyte specific genes. We screened unigenes for repetitive sequences to identify 548 potentially-amplifiable simple sequence repeat loci and 689 expressed transposable elements.ConclusionsThis study is the first comprehensive transcriptome analysis for a fern and represents an important scientific resource for comparative evolutionary and functional genomics studies in land plants. We demonstrate the utility of high-throughput sequencing of a normalized cDNA library for de novo transcriptome characterization and gene discovery in a non-model plant.

Evaluation of atpB nucleotide sequences for phylogenetic studies of ferns and other pteridophytes.

Inferring basal relationships among vascular plants poses a major challenge to plant systematists. The divergence events that describe these relationships occurred long ago and considerable homoplasy has since accrued for both molecular and morphological characters. A potential solution is to examine phylogenetic analyses from multiple data sets. Here I present a new source of phylogenetic data for ferns and other pteridophytes. I sequenced the chloroplast gene atpB from 23 pteridophyte taxa and used maximum parsimony to infer relationships. A 588-bp region of the gene appeared to contain a statistically significant amount of phylogenetic signal and the resulting trees were largely congruent with similar analyses of nucleotide sequences from rbcL. However, a combined analysis of atpB plus rbcL produced a better resolved tree than did either data set alone. In the shortest trees, leptosporangiate ferns formed a monophyletic group. Also, I detected a well-supported clade of Psilotaceae (Psilotum and Tmesipteris) plus Ophioglossaceae (Ophioglossum and Botrychium). The demonstrated utility of atpB suggests that sequences from this gene should play a role in phylogenetic analyses that incorporate data from chloroplast genes, nuclear genes, morphology, and fossil data.

Chloroplast-DNA and allozymic variation in diploid and autotetraploid Heuchera grossulariifolia (Saxifragaceae).

Diploid and autotetraploid populations of Heuchera grossulariifolia occur throughout mountainous regions of the Pacific Northwest. Controlled greenhouse crosses indicated that the two cytotypes are largely reproductively isolated. Fourteen diploid and 11 tetraploid populations were analyzed electrophoretically. Individual tetraploid plants expressed up to four alleles per isozyme locus, and tetraploid populations had significantly higher levels of heterozygosity than diploids. Mean observed heterozygosity was 0.159 for tetraploid populations and 0.058 for diploid populations. The patterns of allelic distribution between cytotypes suggested multiple origins of autotetraploids. This hypothesis was supported by restriction-site analysis of chloroplast-DNA (cpDNA) variation which indicated that there had been at least three independent origins of tetraploids. Electrophoretic data, in conjunction with a cpDNA-based phylogeny and geographic distribution of populations, suggest that autopolyploid populations evolved several times as migration of diploids occurred down river systems. This study further supports the contention that autopolyploidy can be a common and successful speciation process in some groups of plants.

The evolution of chloroplast genes and genomes in ferns

Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some new plastome sequence data. We review what we know about the evolutionary history of plastome structure across the fern phylogeny and we compare plastome organization and patterns of evolution in ferns to those in seed plants. A large clade of ferns is characterized by a plastome that has been reorganized with respect to the ancestral gene order (a similar order that is ancestral in seed plants). We review the sequence of inversions that gave rise to this organization. We also explore global nucleotide substitution patterns in ferns versus those found in seed plants across plastid genes, and we review the high levels of RNA editing observed in fern plastomes.

Unfurling Fern Biology in the Genomics Age

Twenty-first century technology is addressing many of the questions posed by 20th-century biology. Although the new approaches, especially those involving genomic data and bioinformatic tools, were first applied to model organisms, they are now stretching across the tree of life. Here, we review some recent revelations in the ferns. We first examine how DNA sequence data have contributed to our understanding of fern phylogeny. We then address evolution of the fern plastid genome, including reports of high levels of RNA editing. Recent studies are also shedding light on the evolution of fern nuclear genomes. Initial analyses of genomic data suggest that despite their very high chromosome numbers homosporous ferns may have experienced relatively few rounds of genome duplication. Genomic data are enabling researchers to examine speciation rates and the mechanisms underlying the formation of new fern species. We also describe genetic tools that have been used to study gene function and development in ferns. Recent findings in fern biology are providing insights that are not only pertinent to this major component of the land flora but can also help to provide an improved evolutionary context for research on flowering plants.

Phylogenetic Relaitionships of the Enigmatic Fern Families Hymenophyllopsidaceae and Lophosocoriaceae: Evidence From rbcL Nucleotide Sequences

Nucleotide sequences fromrbcL were used to infer relationships of Lophosoriaceae and Hymenophyllopsidaceae. The phylogenetic positions of these two monotypic fern families have been debated, and neither group had been included in recent molecular systematic studies of ferns. Maximum parsimony analysis of our data supported a sister relationship betweenLophosoria andDicksonia, and also betweenHymenophyllopsis andCyathea. Thus, both newly-examined families appear to be part of a previously characterized and well-supported clade of tree ferns. The inferred relationships ofLophosoria are consistent with most (but not all) recent treatments. However,Hymenophyllopsis includes only small delicate plants superficially similar to filmy ferns (Hymenophyllaceae), very different from the large arborescent taxa. Nevertheless, some synapomorphic characteristics are shared with the tree fern clade. Further studies on gametophytes ofHymenophyllopsis are needed to test these hypotheses of relationship.

POLLEN TRANSFER BY NATURAL HYBRIDS AND PARENTAL SPECIES IN AN IPOMOPSIS HYBRID ZONE

Models of hybrid zones differ in their assumptions about the relative fitnesses of hybrids and the parental species. These fitness relationships determine the form of selection across the hybrid zone and, along with gene flow, the evolutionary dynamics and eventual outcome of natural hybridization. We measured a component of fitness, export and receipt of pollen in single pollinator visits, for hybrids between the herbaceous plants Ipomopsis aggregata and I. tenuituba and for both parental species. In aviary experiments with captive hummingbirds, hybrid flowers outperformed flowers of both parental species by receiving more pollen on the stigma. Although hummingbirds were more effective at removing pollen from anthers of I. aggregata, hybrid flowers matched both parental species in the amount of pollen exported to stigmas of other flowers. These patterns of pollen transfer led to phenotypic stabilizing selection, during that stage of the life cycle, for a stigma position intermediate between that of the two species and to directional selection for exserted anthers. Pollen transfer between the species was high, with flowers of I. aggregata exporting pollen equally successfully to conspecific and I. tenuituba flowers. Although this study showed that natural hybrids enjoy the highest quality of pollinator visits, a previous study found that I. aggregata receives the highest quantity of pollinator visits. Thus, the relative fitness of hybrids changes over the life cycle. By combining the results of both studies, pollinator‐mediated selection in this hybrid zone is predicted to be strong and directional, with hybrid fitness intermediate between that of the parental species.