Browsing by Author "Wolf, PG"

Now showing 1 - 9 of 9
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    A classification for extant ferns
    (Taxon, 2006-01-01) Smith, AR; Pryer, KM; Schuettpelz, E; Korall, P; Schneider, H; Wolf, PG
    We present a revised classification for extant ferns, with emphasis on ordinal and familial ranks, and a synopsis of included genera. Our classification reflects recently published phylogenetic hypotheses based on both morphological and molecular data. Within our new classification, we recognize four monophyletic classes, 11 monophyletic orders, and 37 families, 32 of which are strongly supported as monophyletic. One new family, Cibotiaceae Korall, is described. The phylogenetic affinities of a few genera in the order Polypodiales are unclear and their familial placements are therefore tentative. Alphabetical lists of accepted genera (including common synonyms), families, orders, and taxa of higher rank are provided.
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    An exploration into fern genome space
    (Genome Biology and Evolution, 2015) Wolf, PG; Sessa, EB; Marchant, DB; Li, F; Rothfels, CJ; Sigel, EM; Gitzendanner, MA; Visger, CJ; Banks, JA; Soltis, DE
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    An Exploration into Fern Genome Space.
    (Genome Biol Evol, 2015-08-26) Wolf, PG; Sessa, EB; Marchant, DB; Li, F; Rothfels, CJ; Sigel, EM; Gitzendanner, MA; Visger, CJ; Banks, JA; Soltis, DE
    Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.
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    Evolution of vascular plant body plans: a phylogenetic perspective
    (Developmental genetics and plant evolution, 2002) Schneider, H; Pryer, KM; Cranfill, R; Smith, AR; Wolf, PG
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    Fern classification
    (2008-01-01) Smith, AR; Pryer, KATHLEENM; Schuettpelz, ERIC; Korall, P; Schneider, HARALD; Wolf, PG
    © Cambridge University Press 2008 and Cambridge University Press 2009. Introduction and historical summary Over the past 70 years, many fern classifications, nearly all based on morphology, most explicitly or implicitly phylogenetic, have been proposed. The most complete and commonly used classifications, some intended primarily as herbarium (filing) schemes, are summarized in Table 16.1, and include: Christensen (1938), Copeland (1947), Holttum (1947, 1949), Nayar (1970), Bierhorst (1971), Crabbe et al. (1975), Pichi Sermolli (1977), Ching (1978), Tryon and Tryon (1982), Kramer (in Kubitzki, 1990), Hennipman (1996), and Stevenson and Loconte (1996). Other classifications or trees implying relationships, some with a regional focus, include Bower (1926), Ching (1940), Dickason (1946), Wagner (1969), Tagawa and Iwatsuki (1972), Holttum (1973), and M.ckel (1974). Tryon (1952) and Pichi Sermolli (1973) reviewed and reproduced many of these and still earlier classifications, and Pichi Sermolli (1970, 1981, 1982, 1986) also summarized information on family names of ferns. Smith (1996) provided a summary and discussion of recent classifications. With the advent of cladistic methods and molecular sequencing techniques, there has been an increased interest in classifications reflecting evolutionary relationships. Phylogenetic studies robustly support a basal dichotomy within vascular plants, separating the lycophytes (less than 1% of extant vascular plants) from the euphyllophytes (Figure 16.1; Raubeson and Jansen, 1992, Kenrick and Crane, 1997; Pryer et al., 2001a, 2004a, 2004b; Qiu et al., 2006). Living euphyllophytes, in turn, comprise two major clades: spermatophytes (seed plants), which are in excess of 260000 species (Thorne, 2002; Scotland and Wortley, 2003), and ferns (sensu Pryer et al. 2004b), with about 9000 species, including horsetails, whisk ferns, and all eusporangiate and leptosporangiate ferns.
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    Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants.
    (Nature, 2001-02) Pryer, KM; Schneider, H; Smith, AR; Cranfill, R; Wolf, PG; Hunt, JS; Sipes, SD
    Most of the 470-million-year history of plants on land belongs to bryophytes, pteridophytes and gymnosperms, which eventually yielded to the ecological dominance by angiosperms 90 Myr ago. Our knowledge of angiosperm phylogeny, particularly the branching order of the earliest lineages, has recently been increased by the concurrence of multigene sequence analyses. However, reconstructing relationships for all the main lineages of vascular plants that diverged since the Devonian period has remained a challenge. Here we report phylogenetic analyses of combined data--from morphology and from four genes--for 35 representatives from all the main lineages of land plants. We show that there are three monophyletic groups of extant vascular plants: (1) lycophytes, (2) seed plants and (3) a clade including equisetophytes (horsetails), psilotophytes (whisk ferns) and all eusporangiate and leptosporangiate ferns. Our maximum-likelihood analysis shows unambiguously that horsetails and ferns together are the closest relatives to seed plants. This refutes the prevailing view that horsetails and ferns are transitional evolutionary grades between bryophytes and seed plants, and has important implications for our understanding of the development and evolution of plants.
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    Metaxya lanosa, a second species in the genus and fern family Metaxyaceae
    (Systematic Botany, 2001-10-11) Smith, AR; Tuomisto, H; Pryer, KM; Hunt, JS; Wolf, PG
    We describe and illustrate Metaxya lanosa, the second known species in the genus and the fern family Metaxyaceae (Pteridophyta). It is currently known from four different watersheds in Amazonian Peru and Venezuela. It can be distinguished readily from M. rostrata by the noticeably woolly-hairy stipes and rachises (hairs red-brown or orange-brown and easily abraded), broader, more elliptic pinnae, cartilaginous and whitish pinna margins, more distinct veins abaxially, and longer pinna stalks, especially on the distal pinnae, rbcL data from a very limited sampling are ambiguous but do not reject support for the recognition of at least two species within Metaxya.
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    Phylogenetic relationships of the enigmatic fern families Hymenophyllopsidaceae and Lophosoriaceae: Evidence from rbcL nucleotide sequences
    (Plant Systematics and Evolution, 1999-01-01) Wolf, PG; Sipes, SD; White, MR; Martines, ML; Pryer, KM; Smith, AR; Ueda, K
    Nucleotide sequences from rbcL were used to infer relationships of Lophosoriaceae and Hymenophyllopsidaceae. The phylogenetic positions of these two monotypic fern families have been debated, and neither group had been included in recent molecular systematic studies of ferns. Maximum parsimony analysis of our data supported a sister relationship between Lophosoria and Dicksonia, and also between Hymenophyllopsis and Cyathea. Thus, both newly-examined families appear to be part of a previously characterized and well-supported clade of tree ferns. The inferred relationships of Lophosoria are consistent with most (but not all) recent treatments. However, Hymenophyllopsis includes only small delicate plants superficially similar to filmy ferns (Hymenophyllaceae), very different from the large arborescent taxa. Nevertheless, some synapomorphic characteristics are shared with the tree fern clade. Further studies on gametophytes of Hymenophyllopsis are needed to test these hypotheses of relationship.
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    The evolution of chloroplast genes and genomes in ferns.
    (Plant molecular biology, 2011-07) Wolf, PG; Der, JP; Duffy, AM; Davidson, JB; Grusz, AL; Pryer, KM
    Most of the publicly available data on chloroplast (plastid) genes and genomes come from seed plants, with relatively little information from their sister group, the ferns. Here we describe several broad evolutionary patterns and processes in fern plastid genomes (plastomes), and we include some new plastome sequence data. We review what we know about the evolutionary history of plastome structure across the fern phylogeny and we compare plastome organization and patterns of evolution in ferns to those in seed plants. A large clade of ferns is characterized by a plastome that has been reorganized with respect to the ancestral gene order (a similar order that is ancestral in seed plants). We review the sequence of inversions that gave rise to this organization. We also explore global nucleotide substitution patterns in ferns versus those found in seed plants across plastid genes, and we review the high levels of RNA editing observed in fern plastomes.