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Strong selective pressures imposed by drought-prone habitats have contributed to extensive morphological convergence among the 400 + species of cheilanthoid ferns (Pteridaceae). As a result, generic circumscriptions based exclusively on macromorphology often prove to be non-monophyletic. Ongoing molecular phylogenetic analyses are providing the foundation for a revised classification of this challenging group and have begun to clarify its complex evolutionary history. As part of this effort, we generated and analyzed DNA sequence data for three plastid loci (rbcL, atpA, and the intergenic spacer trnG-trnR) for the myriopterid clade, one of the largest monophyletic groups of cheilanthoid ferns. This lineage encompasses 47 primarily North and Central American taxa previously included in Cheilanthes but now placed in the recircumscribed genus Myriopteris. Here, we infer a phylogeny for the group and examine key morphological characters across this phylogeny. We also include a brief discussion of the three well-supported Myriopteris subclades, along with a review of reproductive mode and known ploidy levels for members of this early diverging lineage of cheilanthoid ferns.

Homosporous ferns have extremely high chromosome numbers relative to flowering plants, but the species with the lowest chromosome numbers show gene expression patterns typical of diploid organisms, suggesting that they may be diploidized ancient polyploids. To investigate the role of polyploidy in fern genome evolution, and to provide permanent genetic resources for this neglected group, we constructed a high-resolution genetic linkage map of the homosporous fern model species, Ceratopteris richardii (n = 39). Linkage map construction employed 488 doubled haploid lines (DHLs) that were genotyped for 368 RFLP, 358 AFLP, and 3 isozyme markers. Forty-one linkage groups were recovered, with average spacing between markers of 3.18 cM. Most loci (∼76%) are duplicated and most duplicates occur on different linkage groups, indicating that as in other eukaryotic genomes, gene duplication plays a prominent role in shaping the architecture of fern genomes. Although past polyploidization is a potential mechanism for the observed abundance of gene duplicates, a wide range in the number of gene duplicates as well as the absence of large syntenic regions consisting of duplicated gene copies implies that small-scale duplications may be the primary mode of gene duplication in C. richardii. Alternatively, evidence of past polyploidization(s) may be masked by extensive chromosomal rearrangements as well as smaller-scale duplications and deletions following polyploidization(s).

Biological factors involved in reproductive barriers between two divergent races of Ceratopteris richardii were investigated. We used a combination of spore germination rates, QTL analysis of spore germination rates, and transmission ratio distortion (TRD) of 729 RFLPs, AFLPs, and isozyme markers distributed across the genome on the basis of hybrid populations of 488 doubled haploid lines (DHLs) and 168 F2's. Substantial reproductive barriers were found between the parental races, predominantly in the form of spore inviability (23.7% F1 spore viability). Intrinsic genetic factors such as Bateson–Dobzhansky–Muller (BDM) incompatibilities involving both nuclear–nuclear and nuclear–cytoplasmic factors and chromosomal rearrangements appear to contribute to intrinsic postzygotic isolation. The genomewide distribution patterns of TRD loci support the hypothesis that reproductive barriers are a byproduct of divergence in allopatry and that the strong reproductive barriers are attributable to a small number of genetic elements scattered throughout the genome.

Nucleotide sequences of the chloroplast-encoded rbcL gene were determined for all five species of the onocleoid ferns (Dryopteridaceae tribe Onocleeae), including both varieties of Onoclea sensibilis, and for outgroup member Blechnum glandulosum. Together with GenBank sequences of three additional onocleoid accessions and four additional taxa representing the outgroup Blechnaceae, these were analyzed cladistically under the optimality criteria of maximum parsimony and maximum likelihood. Maximum parsimony yielded a single most-parsimonious tree with the three accessions of Onoclea sensibilis var. sensibilis left as an unresolved trichotomy. Maximum likelihood yielded a single set of three optimal trees whose only topological variation was in the trivial positioning of the three accessions of Onoclea sensibilis var. sensibilis relative to each other. Thus tree topologies of the onocleoid ingroup under maximum parsimony and maximum likelihood were completely congruent. Matteuccia orientalis and M. intermedia formed the basalmost ingroup clade strongly separated from the remaining taxa and sister to them. Onoclea sensibilis is strongly separated from its sister clade of Matteuccia struthiopteris plus Onocleopsis hintonii, and the two varieties of Onoclea sensibilis are well differentiated from each other. Matteuccia struthiopteris and Onocleopsis hintonii form the least strongly supported clade. Levels of sequence divergence among onocleoid taxa are compared with values from other taxa, and morphological and chromosomal data used in previous, noncladistic studies of the onocleoids are reevaluated in light of this rbcL phylogeny. Matteuccia orientalis and M. intermedia should be recognized in their own genus Pentarhizidium, and the previously recognized varieties of Onoclea sensibilis are supported at least at varietal rank and possibly at the rank of species

Genetic linkage mapping based on RFLPs is a valuable genomics tool for studying organisms with no genome sequence information. However, the generally used Southern hybridization method based on the radioisotope^sup 32^P is not ideal for genotyping large mapping populations. We have overcome limitations of the alternative chemiluminescent detection system and developed a high-throughput RFLP genotyping method suitable for large-scale mapping studies of large genomes. Important elements in our process are PCR labeling of probes, complete removal of post-PCR unincorporated nucleotides via column-based purification methods, use of a 1:4 DIG-[11]-dUTP:dTTP ratio, and using a rocker instead of an orbital shaker during hybridization and post-hybridization processing of membranes. Using this method, we mapped the large genome of the homosporous fern speciesCeratopteris richardii by genotyping a mapping population of 513 doubled haploid line (DHL) progeny of a cross between two completely homozygous parental lines. Our genotyping method can robustly detect sub-picogram quantities of DNA fragments from a large number of samples and can be applied to linkage mapping studies of other organisms with large genomes.

Cheilanthoid ferns (Pteridaceae) are a diverse and ecologically important clade, unusual among ferns for their ability to colonize and diversify within xeric habitats. These extreme habitats are thought to drive the extensive evolutionary convergence, and thus morphological homoplasy, that has long thwarted a natural classification of cheilanthoid ferns. Here we present the first multigene phylogeny to focus on taxa traditionally assigned to the large genus Notholaena. New World taxa (Notholaena sensu Tryon) are only distantly related to species occurring in the Old World (Notholaena sensu Pichi Sermolli). The circumscription of Notholaena adopted in recent American floras is shown to be paraphyletic, with species usually assigned to Cheilanthes and Cheiloplecton nested within it. The position of Cheiloplecton is particularly surprising—given its well-developed false indusium and non-farinose blade, it is morphologically anomalous within the \"notholaenoids\". In addition to clarifying natural relationships, the phylogenetic hypothesis presented here helps to resolve outstanding nomenclatural issues and provides a basis for examining character evolution within this diverse, desert-adapted clade.

Molecular data from the chloroplast genome are being used to reconstruct the phylogeny and revise the problematic taxonomy of the xerically adapted cheilanthoid ferns. Chloroplast DNA based phylogenies trace maternal, paternal, or biparental lineages, depending on the mode of inheritance of the chloroplast genome, and instances of all three modes of inheritance are known in the seed plants. Evidence for biparental and uniparental inheritance in ferns has been presented, but the distinction between maternal and paternal uniparental inheritance has not been rigorously made, and the mode of inheritance in cheilanthoid ferns is completely unknown. Based on a natural hybrid population in the cheilanthoid genus Pellaea in which the maternal and paternal derivations of the hybrid are unambiguously known, restriction fragment length polymorphisms of chloroplast DNA demonstrated simple maternal inheritance of the chloroplast genome. This hybrid complex was also examined for restriction fragment length polymorphisms of its mitochondrial DNA, providing the first direct evidence that the mitochondrial genome in ferns is maternally inherited.

Anogramma is a genus of eight putative species with small annual sporophytes and potentially perennating gametophytes. Phylogenetic relationships within the genus as well as its relationships with other putatively taenitidoid genera and with traditionally cheilanthoid Cosentinia vellea have been poorly resolved and are investigated here. Maximum parsimony, maximum likelihood, and Bayesian inference analyses of rbcL sequences were used to test 1) the monophyly of Anogramma, 2) support for the proposed specific distinctness of A. guatemalensis and A. caespitosa from A. leptophylla, and 3) the asserted close (sister) relationship between Anogramma and Pityrogramma, as well as to infer the phylogenetic relationships among these genera. Results reveal that Anogramma in the traditional sense is polyphyletic. Anogramma guatemalensis and A. caespitosa nest within A. leptophylla. Pityrogramma is not sister to Anogramma as a whole but only to A. chaerophylla and A. novogaliciana. Anogramma osteniana is deeply separated from its traditional congeners and the new combination Jamesonia osteniana (Dutra) Gastony is made. Cosentinia vellea should not be subsumed within Cheilanthes but instead should be considered a taenitidoid genus closely related to A. leptophylla and A. lorentzii. Neighbor joining analysis of Amplified Fragment Length Polymorphism data sets inferred relationships among the A. leptophylla accessions, embedding A. guatemalensis and A. caespitosa in respective New World and Old World clades of A. leptophylla.