Phylogenetic relationships of extant ferns based on evidence from morphology and rbcL sequences

We present the first cladistic analysis of extant ferns based on morphological characters. Our data set consisted of 77 vegetative and reproductive morphological/anatomical characters recorded on a broad sampling of 50 extant pteridophyte taxa, with representatives of all major fern groups, and one seed plant (Cycas). An annotated list of both retained and excluded morphological characters is presented. Results from the morphological analysis are compared with an independent analysis of rbcL data carried out here for the same set of pteridophyte taxa. Finally, we analyze a combined (morphological and molecular) data set. All three data sets were analyzed using maximum parsimony. Two separate sets of analyses using different taxon combinations were conducted on each of the three data sets. Analysis 1 focused on phylogenetic relationships of ferns only (Filicopsida, Botrychium, and Angiopteris), using Cycas as an outgroup representative from the seed plants. Analysis 2 focused on phylogenetic relationships of pteridophytes (Filicopsida, Angiopteris, Botrychium, Equisetum, Psilotum), using Lycopodium as the outgroup. In both sets of analyses, the combined data set provided the most robustly supported hypothesis of relationships. Results from the combined data set in Analysis 1 provided strong bootstrap support for the monophyly of the following clades: leptosporangiate ferns (with Osmunda as the most basal leptosporangiate fern), heterosporous ferns, Cheiropleuria-Dipteris, Diplopterygium-Stromatopteris, tree ferns, schizaeoid ferns, pteridoid ferns, and a large clade consisting of a derived group of leptosporangiate ferns that excludes dennstaedtioids and pteridoids. Various smaller clades within some of these larger clades also have strong support. The dennstaedtioid ferns are paraphyletic. We use the results of the combined data set in Analysis 1 to examine character evolution within the leptosporangiate ferns. Results from the combined data set in Analysis 2 indicated robust support for essentially the same fern clades as the combined data set in Analysis 1. In both Analyses 1 and 2, bootstrap support for the leptosporangiate fern clade is much greater using the combined data set than when either the morphological or, particularly, the molecular data set is analyzed separately. Relationships among major groups of pteridophytes at the base of the tree (Botrychium, Angiopteris, Psilotum, Equisetum, Lycopodium) were poorly supported by the combined data in Analysis 2, except for a weak association between Botrychium and Psilotum. We are convinced from this study of the value of using both molecular and morphological data sets in combination as well as separately. A synthetic approach that integrates paleobotanical and neobotanical data will be of greatest interest in further elucidating the phylogenetic relationships of pteridophytes.