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Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.

Significance Despite being one of the oldest groups of land plants, the majority of living ferns resulted from a relatively recent diversification following the rise of angiosperms. To exploit fully the new habitats created by angiosperm-dominated ecosystems, ferns had to evolve novel adaptive strategies to cope with the low-light conditions exerted by the angiosperm canopy. Neochrome, an unconventional photoreceptor that allows ferns to “see the light” better, was likely part of the solution. Surprisingly, we discovered that fern neochrome was derived from a bryophyte lineage via horizontal gene transfer (HGT). This finding not only provides the first evidence that a plant-to-plant HGT can have a profound evolutionary impact but also has implications for the evolution of photosensory systems in plants.

BackgroundMolecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns—the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales.Principal FindingsWe present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs—curated broadly across ferns—that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group.ConclusionsThe 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.

The genus Paliurus, recognized by its distinctive orbicular-winged fruit, is well represented in the fossil record of the Northern Hemisphere. Fruits assignable to Paliurus are known from the Tertiary of North America, Europe, and Asia, while extant species are limited to Eurasia. We examined variation in fruit morphology among extant species as a basis for interpreting fossil fruits. Although Paliurus fruits are diverse in size, shape, and sculpture, there are few consistent criteria for demarcating species. On the basis of morphometric analysis, we recommend synonymy of most fossil fruits under the name Paliurus favonii. New records for this species are reported from the Eocene and Miocene of North America, and a distinctive new species from the Middle Eocene of North America, Paliurus clarnensis, is introduced. The genus ranges from the Middle Eocene to Late Miocene in North America, the Late Eocene to Pleistocene in Asia, and from the Oligocene to Pliocene in Europe. The fossil record indicates range expansion over the Northern Hemisphere during the Eocene and Miocene, possibly via high latitude migratory routes, followed by dramatic range contraction near the close of the Miocene, including extinction from central Asia and North America.