Browsing by Subject "divergence time estimates"
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Item Open Access 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, JAlthough 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.Item Open Access Phylogeny and divergence time estimates for the fern genus Azolla (Salviniaceae)(International Journal of Plant Sciences, 2007-10-22) Metzgar, JS; Schneider, H; Pryer, KMA phylogeny for all extant species of the heterosporous fern genus Azolla is presented here based on more than 5000 base pairs of DNA sequence data from six plastid loci (rbcL, atpB, rps4, trnL-trnF, trnG-trnR, and rps4-trnS). Our results are in agreement with other recent molecular phylogenetic hypotheses that support the monophyly of sections Azolla and Rhizosperma and the proposed relationships within section Azolla. Divergence times are estimated within Azolla using a penalized likelihood approach, integrating data from fossils and DNA sequences. Penalized likelihood analyses estimate a divergence time of 50.7 Ma (Eocene) for the split between sections Azolla and Rhizosperma, 32.5 Ma (Oligocene) for the divergence of Azolla nilotica from A. pinnata within section Rhizosperma, and 16.3 Ma (Miocene) for the divergence of the two lineages within section Azolla (the A. filiculoides + A. rubra lineage from the A. caroliniana + A. microphylla + A. mexicana complex). © 2007 by The University of Chicago. All rights reserved.Item Open Access Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences.(American journal of botany, 2004-10) Pryer, Kathleen M; Schuettpelz, Eric; Wolf, Paul G; Schneider, Harald; Smith, Alan R; Cranfill, RaymondThe phylogenetic structure of ferns (= monilophytes) is explored here, with a special focus on the early divergences among leptosporangiate lineages. Despite considerable progress in our understanding of fern relationships, a rigorous and comprehensive analysis of the early leptosporangiate divergences was lacking. Therefore, a data set was designed here to include critical taxa that were not included in earlier studies. More than 5000 bp from the plastid (rbcL, atpB, rps4) and the nuclear (18S rDNA) genomes were sequenced for 62 taxa. Phylogenetic analyses of these data (1) confirm that Osmundaceae are sister to the rest of the leptosporangiates, (2) resolve a diverse set of ferns formerly thought to be a subsequent grade as possibly monophyletic (((Dipteridaceae, Matoniaceae), Gleicheniaceae), Hymenophyllaceae), and (3) place schizaeoid ferns as sister to a large clade of "core leptosporangiates" that includes heterosporous ferns, tree ferns, and polypods. Divergence time estimates for ferns are reported from penalized likelihood analyses of our molecular data, with constraints from a reassessment of the fossil record.