Ferns are the second-most diverse lineage of vascular plants on Earth, yet the best-sampled time-calibrated phylogeny of the group to date includes fewer than 5% of global diversity and was published seven years ago. We present a time-calibrated phylogeny that includes nearly half of extant fern diversity. Our results are evaluated in the context of previous studies and the fossil record, and we develop new hypotheses about the radiation of leptosporangiate ferns. We used sequence data from six chloroplast regions for nearly 4000 species of ferns to generate the most comprehensive phylogeny of the group ever published. We calibrate the phylogeny with twenty-six fossils and use an array of phylogenetic methods to resolve phylogenetic relationships, estimate divergence times, and infer speciation, extinction, and net diversification rates. We infer a mid-late Silurian origin for ferns (including horsetails) and an early Carboniferous origin for leptosporangiate ferns. Most derived fern families appeared in the Cretaceous and persisted for millions of years before rapidly diversifying in the Cenozoic. We find no evidence of differential rates of diversification among terrestrial and epiphytic species. Our findings challenge previous hypotheses on the evolutionary history of ferns and present a new paradigm for their Cenozoic radiation. We estimate earlier divergences for most fern lineages than were reported in previous studies and provide evidence of extended persistence of major fern lineages prior to rapid diversification in the last fifty million years.

We present a family–level classification for the eupolypod II clade of leptosporangiate ferns, one of the two major lineages within the Eupolypods, and one of the few parts of the fern tree of life where family–level relationships were not well understood at the time of publication of the 2006 fern classification by Smith & al. Comprising over 2500 species, the composition and particularly the relationships among the major clades of this group have historically been contentious and defied phylogenetic resolution until very recently. Our classification reflects the most current available data, largely derived from published molecular phylogenetic studies. In comparison with the five–family (Aspleniaceae, Blechnaceae, Onocleaceae, Thelypteridaceae, Woodsiaceae) treatment of Smith & al., we recognize 10 families within the eupolypod II clade. Of these, Aspleniaceae, Thelypteridaceae, Blechnaceae, and Onocleaceae have the same composition as treated by Smith & al. Woodsia–ceae, which Smith & al. acknowledged as possibly non–monophyletic in their treatment, is circumscribed here to include only Woodsia and its segregates; the other “woodsioid” taxa are divided among Athyriaceae, Cystopteridaceae, Diplaziopsidaceae, Rhachidosoraceae, and Hemidictyaceae. We provide circumscriptions for each family, which summarize their morphological, geographical, and ecological characters, as well as a dichotomous key to the eupolypod II families. Three of these families— Diplaziopsidaceae, Hemidictyaceae, and Rhachidosoraceae—were described in the past year based on molecular phylogenetic analyses; we provide here their first morphological treatment.

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The emergence of angiosperm-dominated tropical forests in the Cretaceous led to major shifts in the composition of biodiversity on Earth. Among these was the rise to prominence of epiphytic plant lineages, which today comprise an estimated one-quarter of tropical vascular plant diversity. Among the most successful epiphytic groups is the Polypodiaceae, which comprises an estimated 1500 species and displays a remarkable breadth of morphological and ecological diversity. Using a time-calibrated phylogeny for 417 species, we characterized macroevolutionary patterns in the family, identified shifts in diversification rate, and identified traits that are potential drivers of diversification. We find high diversification rates throughout the family, evidence for a radiation in a large clade of Paleotropical species, and support for increased rates of diversification associated with traits including chlorophyllous spores and noncordiform gametophytes. Contrary to previous hypotheses, our results indicate epiphytic species and groups with humus-collecting leaves diversify at lower rates than the family as a whole. We find that diversification rates in the Polypodiaceae are positively correlated with changes in elevation. Repeated successful exploration of novel habitat types, rather than morphological innovation, appears to be the primary driver of diversification in this group.

The integrated approach synthesizes morphological studies with current phylogenetic hypotheses and provides explicit statements of character evolution in the eupolypod II fern families. Strong character support is found for previously recognized clades, whereas few characters support previously unrecognized clades. Sorus position appears to be less complicated than previously hypothesized, and linear sori restricted to one side of the vein support the clade comprising Aspleniaceae, Diplaziopsidaceae, Hemidictyaceae and Rachidosoraceae - a lineage only recently identified. Despite x =41 being a frequent number among extant species, to our knowledge it has not previously been demonstrated as the ancestral state. This is the first synapomorphy proposed for the eupolypod clade, a lineage comprising 67 % of extant fern species. This study provides some of the first hypotheses of character evolution at the family level and above in light of recent phylogenetic results, and promotes further study in an area that remains open for original observation.

Based on a worldwide phylogenetic framework filling the taxonomic gap of Madagascar and surrounding islands of the Western Indian Ocean (WIO), we revisited the systematics of grammitid fern species (Polypodiaceae). We also investigated the biogeographic origin of the extant diversity in Madagascar and estimated the relative influence of vicariance, long-distance dispersals (LDD) and in situ diversification. Phylogenetic inferences were based on five plastid DNA regions (atpB, rbcL, rps4-trnS, trnG-trnR, trnL-trnF) and the most comprehensive taxonomic sampling ever assembled (224 species belonging to 31 out of 33 recognized grammitids genera). 31 species from Madagascar were included representing 87% of the described diversity and 77% of the endemics. Our results confirmed a Paleotropical clade nested within an amphi-Atlantic grade. In addition, we identified three new major clades involving species currently belonging to Grammitis s.l., Ctenopterella and Enterosora. We resolved for the first time Grammitis s.s. as monophyletic, and Ctenopterella (newly tested here) and Enterosora as polyphyletic. The Neotropical genus Moranopteris was shown to also occur in Madagascar through a newly discovered species. Most importantly, we suggest a >30% inflation of the species number in the WIO due to the hidden diversity in >10 cryptic lineages, best explained by high morphological homoplasy. Molecular dating and ancestral areas reconstruction allowed identifying the Neotropics as the predominant source of LDD to the African-WIO region, with at least 12 colonization events within the last 20Ma. Repeated eastward migrations may be explained by transoceanic westerly winds transporting the dust-like spores. Tropical Asia s.l. would also have played a (minor) role through one dispersal event to Madagascar at the end of the Oligocene. Last, within the complex Malagasy region made of a mosaic of continental and oceanic islands located close to the African continent, we showed that contrary to theoretical expectations and empirical evidence in angiosperms, Africa does not act as a dispersal source and Madagascar seems to have a more important influence on the regional dynamics: we observed both in situ species diversification and dispersal out of Madagascar. This influence also extends beyond the region, since one dispersal event probably originated from Madagascar and reached the Subantarctic island of Amsterdam.

Aim Gondwanan vicariance, boreotropical migration and long‐distance dispersal have been posited as alternative hypotheses explaining the tropical distribution patterns and diversifications in many fern groups. Here, the historical biogeography of Diplazium is reconstructed to evaluate the impact of these biogeographical processes in shaping the modern tropical disjunctions. Location World‐wide with a focus on tropical forest habitats. Methods Divergence times were estimated by analysing nucleotide sequences of seven plastid DNA regions (atpA, atpB, matK, rbcL, rps4, rps4–trnS and trnL–F) from 123 species of Diplazium and its allied genera, using a Bayesian relaxed clock method and three fossil calibrations. The ancestral areas were reconstructed using the likelihood dispersal–extinction–cladogenesis (DEC) approach. Results The crown group of Diplazium was estimated to have originated in Eurasia and undergone an initial diversification in the Northern Hemisphere around 41.7 Ma [95% highest posterior density (HPD): 34–49 Ma] during the Eocene. Two disjunct events between the Old and New World were identified: one in subgenus Diplazium around the Eocene–Oligocene boundary (31.2 Ma, 95% HPD: 25–38 Ma), and the other in subgenus Callipteris during the middle Miocene (12.6 Ma, 95% HPD: 15–23 Ma). Furthermore, Palaeotropical disjunctions in subgenus Callipteris are indicative of multiple dispersal events during the Miocene. Main conclusions The evolutionary history of Diplazium involves a variety of biogeographical scenarios. Early diversification of Diplazium in the Northern Hemisphere during the Eocene corresponds with the migration from Eurasia to North America over land bridges as a member of the boreotropical flora. The current tropical amphi‐Pacific disjunctions in subgenus Diplazium can be better explained by the disruption of boreotropical belt, however, long‐distance dispersal between Eurasia and tropical America cannot be ruled out. Island‐hopping and trans‐Pacific dispersals followed by speciation characterize the disjunctions and diversifications of subgenus Callipteris during the Neogene. Gondwanan vicariance is not supported by any of our results.