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.

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A classification for extant ferns

The phylogenetic structure of ferns (5 monilophytes) is explored here, with a special focus on the early divergences among leptosporangiate lineages. Despite considerable progress in our understanding of fern relationships, a rigorous and comprehensive analysis of the early leptosporangiate divergences was lacking. Therefore, a data set was designed here to include critical taxa that were not included in earlier studies. More than 5000 bp from the plastid (rbcL, atpB, rps4) and the nuclear (18S rDNA) genomes were sequenced for 62 taxa. Phylogenetic analyses of these data (1) confirm that Osmundaceae are sister to the rest of the leptosporangiates, (2) resolve a diverse set of ferns formerly thought to be a subsequent grade as possibly monophyletic (((Dipteridaceae, Matoniaceae), Gleicheniaceae), Hymenophyllaceae), and (3) place schizaeoid ferns as sister to a large clade of ‘‘core leptosporangiates’’ that includes heterosporous ferns, tree ferns, and polypods. Divergence time estimates for ferns are reported from penalized likelihood analyses of our molecular data, with constraints from a reassessment of the fossil record.

Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences

In an effort to obtain a solid and balanced approximation of global fern phylogeny to serve as a tool for addressing large-scale evolutionary questions, we assembled and analyzed the most inclusive molecular dataset for leptosporangiate ferns to date. Three plastid genes (rbcL, atpB, atpA), totaling more than 4,000 bp, were sequenced for each of 400 leptosporangiate fern species (selected using a proportional sampling approach) and five outgroups. Maximum likelihood analysis of these data yielded an especially robust phylogeny: 80% of the nodes were supported by a maximum likelihood bootstrap percentage ≥ 70. The scope of our analysis provides unprecedented insight into overall fern relationships, not only delivering additional support for the deepest leptosporangiate divergences, but also uncovering the composition of more recently emerging clades and their relationships to one another.

Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes

Land plants exhibit a significant evolutionary plasticity in their mitochondrial DNA (mtDNA), which contrasts with the more conservative evolution of their chloroplast genomes. Frequent genomic rearrangements, the incorporation of foreign DNA from the nuclear and chloroplast genomes, an ongoing transfer of genes to the nucleus in recent evolutionary times and the disruption of gene continuity in introns or exons are the hallmarks of plant mtDNA, at least in flowering plants. Peculiarities of gene expression, most notably RNA editing and trans-splicing, are significantly more pronounced in land plant mitochondria than in chloroplasts. At the same time, mtDNA is generally the most slowly evolving of the three plant cell genomes on the sequence level, with unique exceptions in only some plant lineages. The slow sequence evolution and a variable occurrence of introns in plant mtDNA provide an attractive reservoir of phylogenetic information to trace the phylogeny of older land plant clades, which is as yet not fully resolved. This review attempts to summarize the unique aspects of land plant mitochondrial evolution from a phylogenetic perspective.

The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective

Plant mitochondrial (mt) genomes have long been known to evolve slowly in sequence. Here we show remarkable departure from this pattern of conservative evolution in a genus of flowering plants. Substitution rates at synonymous sites vary substantially among lineages within Plantago. At the extreme, rates in Plantago exceed those in exceptionally slow plant lineages by ≈4,000-fold. The fastest Plantago lineages set a new benchmark for rapid evolution in a DNA genome, exceeding even the fastest animal mt genome by an order of magnitude. All six mt genes examined show similarly elevated divergence in Plantago, implying that substitution rates are highly accelerated throughout the genome. In contrast, substitution rates show little or no elevation in Plantago for each of four chloroplast and three nuclear genes examined. These results, combined with relatively modest elevations in rates of nonsynonymous substitutions in Plantago mt genes, indicate that major, reversible changes in the mt mutation rate probably underlie the extensive variation in synonymous substitution rates. These rate changes could be caused by major changes in any number of factors that control the mt mutation rate, from the production and detoxification of oxygen free radicals in the mitochondrion to the efficacy of mt DNA replication and/or repair.

https://www.pnas.org/content/pnas/101/51/17741.full.pdf

Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants.

A conserved coding region of the mitochondrial nad5 gene (1098–1107 bp of protein coding sequence) was amplified from 30 pteridophytes (26 ferns and 4 fern allies). A group II intron sequence conserved in all ferns except the eu-sporangiate genus Ophioglossum is also present in the whisk fern Psilotum nudum and the lycopod Huperzia selogo, but absent from the horsetails (Equisetum), the seed plants and the bryo-phytes. Phylogenetic trees constructed with different methods consistently suggest several monophyletic units. The conserved group II intron sequence provides valuable additional phylogenetic information. Leptosporangiate ferns are monophyletic with Osmunda as the basal-most branching genus followed by Trichomanes, Matonia and Lygodium. These genera are set distantly apart from other leptosporangiate ferns, including the tree and water ferns, which branch in close proximity. Species of Polypodiaceae, Dryopteridaceae, Thelypteridaceae, Aspleniaceae and Blechnaceae appear in a monophyletic crown group of derived leptosporangiate ferns with Dryopteridaceae as a paraphyletic taxon. Placement of Psilotum in a class of its own receives no support from the mitochondrial sequences, which rather suggest its inclusion among eusporangiate ferns (Ophioglossales). RNA editing is required to correct the genetic information of the nad5 gene in all species investigated and includes the removal of stop codons from the reading frames. The influence of RNA editing on phylogenetic tree construction is investigated and discussed.

T. Teerkorn

Papers

Phylogenetic Information in the Mitochondrial nad5 Gene of Pteridophytes: RNA Editing and Intron Sequences