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.

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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.

New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. METHODS: We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages. RESULTS: Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics. CONCLUSIONS: A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.

SummaryHomosporous vascular plants utilize three different mating systems, one of which, gametophytic selfing, is an extreme form of inbreeding only possible in homosporous groups. This mating system results in complete homozygosity in all progeny and has important evolutionary and ecological implications. Ferns are the largest group of homosporous land plants, and the significance of extreme inbreeding for fern evolution has been a subject of debate for decades.We cultured gametophytes in the laboratory and quantified the relative frequencies of sporophyte production from isolated and paired gametophytes, and examined associations between breeding systems and several ecological and evolutionary traits.The majority of fern species studied show a capacity for gametophytic selfing, producing sporophytes from both isolated and paired gametophytes. While we did not follow sporophytes to maturity to investigate potential detrimental effects of homozygosity at later developmental stages, our results suggest that gametophytic selfing may have greater significance for fern evolution and diversification than has previously been realized.We present evidence from the largest study of mating behavior in ferns to date that the capacity for extreme inbreeding is prevalent in this lineage, and we discuss its implications and relevance and make recommendations for future studies of fern mating systems.

Aim: It is well known that the distribution of species diversity is spatially heterogeneous, but understanding the factors contributing to this heterogeneity and to the formation of biodiversity hotspots remains a challenge. Here, we seek to improve our understanding of how historical, ecological and evolutionary processes contribute to current patterns of global fern diversity.Location: Worldwide. Taxon: Ferns.Methods: To evaluate the drivers of global fern diversity, we integrate over 800,000 georeferenced species occurrence records of nearly 8000 species, a time-calibrated phylogeny and seven climate and environmental layers. We use these data to summarize diversity and evolutionary patterns at a resolution of 100 × 100 km, and identify hotspots of fern species richness and endemism. We compare these hotspots to neighbouring non-hotspot regions to provide insight into the factors controlling global patterns of fern diversity.Results: Tropical and subtropical mountains harbour a disproportionate amount of species relative to the land area they occupy; 58% of global species richness occur in eight principally montane hotspots together comprising just 7% of Earth's land area.We identify hotspots of fern species richness and endemism that are universally characterized by disproportionately high ecological variation. We demonstrate that total fern species richness scales linearly with available climate space at regional and global scales.Main Conclusions: Areas of high environmental heterogeneity harbour a disproportionate amount of fern species, and global patterns of extant fern diversity reflect the distribution of these areas, especially in mountains at lower latitudes. Persistence of ancient lineages in areas with long-term climatic stability helps explain exceptional endemism in regions such as Malesia.

Tropical mountains are disproportionately biodiverse relative to their surface area, but the processes underlying their exceptional diversity require further study. Here, we use comparative phylogenetic methods to examine the impact of the Andean orogeny on the diversification of Neotropical Phlegmariurus, a species-rich lycophyte clade.We generated a time-calibrated phylogeny of 105 species of Neotropical Phlegmariurus and estimated lineage diversification rates. We tested for correlations between lineage diversification rates and species range size, niche breadth, elevational range amplitude, and mean elevation of occurrence. A recently developed macroevolutionary model was used to incorporate geological data and test for an association between diversification rates and the Andean uplift.Diversification rates of Neotropical Phlegmariurus are negatively correlated with species range size and positively correlated with mean elevation of species occurrence. The rise of the Andes is strongly associated with increased rates of diversification in Neotropical Phlegmariurus during the last 10 Myr.Our study demonstrates the importance of mountain-building events and geographical isolation of alpine populations as drivers of rapid diversification, even in spore-dispersed plants. This work also highlights the usefulness of combined phylogenetic, geological and ecological datasets, and the promise of comparative environment-dependent diversification models in better understanding the evolutionary origins of biodiversity.