Browsing by Subject "SEQUENCE DATA"

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    Is morphology really at odds with molecules in estimating fern phylogeny?
    (Systematic Botany, 2009-07-01) Schneider, H; Smith, AR; Pryer, KM
    Using a morphological dataset of 136 vegetative and reproductive characters, we infer the tracheophyte phylogeny with an emphasis on early divergences of ferns (monilophytes). The dataset comprises morphological, anatomical, biochemical, and some DNA structural characters for a taxon sample of 35 species, including representatives of all major lineages of vascular plants, especially ferns. Phylogenetic relationships among vascular plants are reconstructed using maximum parsimony and Bayesian inference. Both approaches yield similar relationships and provide evidence for three major lineages of extant vascular plants: lycophytes, ferns, and seed plants. Lycophytes are sister to the euphyllophyte clade, which comprises the fern and seed plant lineages. The fern lineage consists of five clades: horsetails, whisk ferns, ophioglossoids, marattioids, and leptosporangiate ferns. This lineage is supported by characters of the spore wall and has a parsimony bootstrap value of 76%, although the Bayesian posterior probability is only 0.53. Each of the five fern clades is well supported, but the relationships among them lack statistical support. Our independent phylogenetic analyses of morphological evidence recover the same deep phylogenetic relationships among tracheophytes as found in previous studies utilizing DNA sequence data, but differ in some ways within seed plants and within ferns. We discuss the extensive independent evolution of the five extant fern clades and the evidence for the placement of whisk ferns and horsetails in our morphological analyses. © 2009 by the American Society of Plant Taxonomists.
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    Phylogeny of Marsileaceous Ferns and Relationships of the Fossil Hydropteris pinnata Reconsidered.
    (International journal of plant sciences, 1999-09) Pryer, KM
    Recent phylogenetic studies have provided compelling evidence that confirms the once disputed hypothesis of monophyly for heterosporous leptosporangiate ferns (Marsileaceae and Salviniaceae). Hypotheses for relationships among the three genera of Marsileaceae (Marsilea, Regnellidium, and Pilularia), however, have continued to be in conflict. The phylogeny of Marsileaceae is investigated here using information from morphology and rbcL sequence data. In addition, relationships among all heterosporous ferns, including the whole-plant fossil Hydropteris pinnata are reconsidered. Data sets of 71 morphological and 1239 rbcL characters for 23 leptosporangiate ferns, including eight heterosporous ingroup taxa and 15 homosporous outgroup taxa, were subjected to maximum parsimony analysis. Morphological analyses were carried out both with and without the fossil Hydropteris, and it was excluded from all analyses with rbcL data. An annotated list of the 71 morphological characters is provided in the appendix. For comparative purposes, the Rothwell and Stockey (1994) data set was also reanalyzed here. The best estimate of phylogenetic relationships for Marsileaceae in all analyses is that Pilularia and Regnellidium are sister taxa and Marsilea is sister to that clade. Morphological synapomorphies for various nodes are discussed. Analyses that included Hydropteris resulted in two most-parsimonious trees that differ only in the placement of the fossil. One topology is identical to the relationship found by Rothwell and Stockey (1994), placing the fossil sister to the Azolla plus Salvinia clade. The alternative topology places Hydropteris as the most basal member of the heterosporous fern clade. Equivocal interpretations for character evolution in heterosporous ferns are discussed in the context of these two most-parsimonious trees. Because of the observed degree of character ambiguity, the phylogenetic placement of Hydropteris is best viewed as unresolved, and recognition of the suborder Hydropteridineae, as circumscribed by Rothwell and Stockey (1994), is regarded as premature. The two competing hypotheses of relationships for heterosporous ferns are also compared with the known temporal distribution of relevant taxa. Stratigraphic fit of the phylogenetic estimates is measured by using the Stratigraphic Consistency Index and by comparison with minimum divergence times.
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    rbcL phylogeny of the fern genus Trichomanes (Hymenophyllaceae), with special reference to Neotropical taxa
    (International Journal of Plant Sciences, 2003-01-01) Dubuisson, JY; Hennequin, S; Douzery, EJP; Cranfill, RB; Smith, AR; Pryer, KM
    In order to estimate evolutionary relationships within the filmy fern genus Trichomanes (Hymenophyllaceae), we performed a phylogenetic analysis using rbcL nucleotide data from 46 species of Trichomanes belonging to all four of C. V. Morton's subgenera: Achomanes, Didymoglossum, Pachychaetum, and Trichomanes. Outgroups included four species of Hymenophyllum in three different subgenera, plus the monotypic genus Cardiomanes, from New Zealand. We find high resolution and robust support at most nodes, regardless of the phylogenetic optimization criterion used (maximum parsimony or maximum likelihood). Two species belonging to Morton's Asiatic sections Callistopteris and Cephalomanes are in unresolved basal positions within Trichomanes s.l., suggesting that rbcL data alone are inadequate for estimating the earliest cladogenetic events. Out of the four Morton trichomanoid subgenera, only subg. Didymoglossum appears monophyletic. Other noteworthy results include the following: (1) lianescent sect. Lacostea is more closely related to sect. Davalliopsis (traditionally placed in subg. Pachychaetum) than to other members of subg. Achomanes; (2) sections Davalliopsis and Lacostea, together with species of the morphologically different subg. Achomanes, make up a strongly supported Neotropical clade; (3) all hemiepiphytes (but not true lianas) and strictly epiphytic or epipetric species (Morton's subgenera Trichomanes and Didymoglossum) group together in an ecologically definable clade that also includes the terrestrial sect. Nesopteris; and (4) sect. Lacosteopsis (sensu Morton) is polyphyletic and comprises two distantly related clades: large hemiepiphytic climbers and small strictly epiphytic/epipetric taxa. Each of these associations is somewhat unexpected but is supported by cytological, geographical, and/or ecological evidence. We conclude that many morphological characters traditionally used for delimiting groups within Trichomanes are, in part, plesiomorphic or homoplastic. Additionally, we discuss probable multiple origins of Neotropical Trichomanes.