A Plastid Phylogeny of the Cosmopolitan Fern Family Cystopteridaceae (Polypodiopsida)

Among the novel results of recent molecular phylogenetic analyses are the unexpectedly close evolutionary relationships of the genera Acystopteris, Cystopteris, and Gymnocarpium, and the phylogenetic isolation of these genera fromWoodsia. As a consequence, these three genera have been removed from Woodsiaceae and placed into their own family, the Cystopteridaceae. Despite the ubiquity of this family in rocky habitats across the northern hemisphere, and its cosmopolitan distribution (occurring on every continent except Antarctica), sampling of the Cystopteridaceae in phylogenetic studies to date has been sparse. Here we assemble a three-locus plastid dataset (matK, rbcL, trnG-R) that includes most recognized species in the family and multiple accessions of widespread taxa from across their geographic ranges. All three sampled genera are robustly supported as monophyletic, Cystopteris is strongly supported as sister to Acystopteris, and those two genera together are sister to Gymnocarpium. The Gymnocarpium phylogeny is deeply divided into three major clades, which we label the disjunctum clade, the robertianum clade, and core Gymnocarpium. The Cystopteris phylogeny, similarly, features four deeply diverged clades: C. montana, the sudetica clade, the bulbifera clade, and the fragilis complex. Acystopteris includes only three species, each of which is supported as monophyletic, with A. taiwaniana sister to the japonica/tenuisecta clade. Our results yield the first species-level phylogeny of the Cystopteridaceae and the first molecular phylogenetic evidence for species boundaries. These data provide an essential foundation for further investigations of complex patterns of geographic diversification, speciation, and reticulation in this family. Keywords—Cosmopolitan species, Cystopteris, fern phylogeny, Gymnocarpium, intralinkage incongruence, species complex. Cystopteris Bernh. and Gymnocarpium Newman—including the bulblet fern, bladder ferns, fragile ferns, and oak ferns (see Fig. 1A–C, E–H)—are among the most frequently encountered and familiar ferns in the northern hemisphere, occurring in most forested and rocky habitats in North America, Europe, and Asia. However, despite their familiarity, their phylogenetic relationships have been contentious. Acystopteris Nakai (Fig. 1D) and Cystopteris have long been considered close relatives, with many authors historically treating them together under a broad concept of Cystopteris (e.g. Tagawa 1935; Blasdell 1963). Prior to the proliferation of molecular evidence, however, most taxonomists did not consider Cystopteris s.l. and Gymnocarpium to be closely allied. Instead, these two taxa usually were assigned to the dryopteroid and athyrioid fern lineages, respectively, with the caveat that they were each morphologically anomalous within those lineages and that their phylogenetic positions were thus uncertain (e.g. Sledge 1973). This confusion regarding the affinities of Cystopteris and Gymnocarpium to other polypod ferns has continued until very recently. For example, when naming the family Cystopteridaceae, Schmakov (2001) included Pseudocystopteris Ching (which belongs in the Athyriaceae; Kato 1977; Sano et al. 2000; Fraser-Jenkins 2008; Liu 2008; Rothfels et al. 2012b). Quite recently, Z. R. Wang (1997), M. L. Wang et al. (2004) and Smith et al. (2006) each advocated familial concepts that grouped Cystopteris and Gymnocarpium with very distantly related taxa (Rothfels