Browsing by Author "Ebihara, A"

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    Divergence times and the evolution of epiphytism in filmy ferns (Hymenophyllaceae) revisited
    (International Journal of Plant Sciences, 2008-11-01) Hennequin, S; Schuettpelz, E; Pryer, KM; Ebihara, A; Dubuisson, J
    Although the phylogeny of the filmy fern family (Hymenophyllaceae) is rapidly coming into focus, much remains to be uncovered concerning the evolutionary history of this clade. In this study, we use two data sets (108-taxon rbcL+ rps4, 204-taxon rbcL) and fossil constraints to examine the diversification of filmy ferns and the evolution of their ecology within a temporal context. Our penalized likelihood analyses (with both data sets) indicate that the initial divergences within the Hymenophyllaceae (resulting in extant lineages) and those within one of the two major clades (trichomanoids) occurred in the early to middle Mesozoic. There was a considerable delay in the crown group diversification of the other major clade (hymenophylloids), which began to diversify only in the Cretaceous. Maximum likelihood and Bayesian character state reconstructions across the broadly sampled single-gene (rbcL) phylogeny do not allow us to unequivocally infer the ancestral habit for the family or for its two major clades. However, adding a second gene (rps4) with a more restricted taxon sampling results in a hypothesis in which filmy ferns were ancestrally terrestrial, with epiphytism having evolved several times independently during the Cretaceous. © 2008 by The University of Chicago. All rights reserved.
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    rbcL and matK earn two thumbs up as the core DNA barcode for ferns.
    (PloS one, 2011-01) Li, F; Kuo, L; Rothfels, CJ; Ebihara, A; Chiou, W; Windham, MD; Pryer, KM
    BACKGROUND: DNA barcoding will revolutionize our understanding of fern ecology, most especially because the accurate identification of the independent but cryptic gametophyte phase of the fern's life history--an endeavor previously impossible--will finally be feasible. In this study, we assess the discriminatory power of the core plant DNA barcode (rbcL and matK), as well as alternatively proposed fern barcodes (trnH-psbA and trnL-F), across all major fern lineages. We also present plastid barcode data for two genera in the hyperdiverse polypod clade--Deparia (Woodsiaceae) and the Cheilanthes marginata group (currently being segregated as a new genus of Pteridaceae)--to further evaluate the resolving power of these loci. PRINCIPAL FINDINGS: Our results clearly demonstrate the value of matK data, previously unavailable in ferns because of difficulties in amplification due to a major rearrangement of the plastid genome. With its high sequence variation, matK complements rbcL to provide a two-locus barcode with strong resolving power. With sequence variation comparable to matK, trnL-F appears to be a suitable alternative barcode region in ferns, and perhaps should be added to the core barcode region if universal primer development for matK fails. In contrast, trnH-psbA shows dramatically reduced sequence variation for the majority of ferns. This is likely due to the translocation of this segment of the plastid genome into the inverted repeat regions, which are known to have a highly constrained substitution rate. CONCLUSIONS: Our study provides the first endorsement of the two-locus barcode (rbcL+matK) in ferns, and favors trnL-F over trnH-psbA as a potential back-up locus. Future work should focus on gathering more fern matK sequence data to facilitate universal primer development.