Browsing by Subject "Plant Sciences"

Now showing 1 - 20 of 53

Open Access
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.
Open Access
A diploids-first approach to species delimitation and interpreting polyploid evolution in the fern genus astrolepis (pteridaceae)
(Systematic Botany, 2010-04-01) Beck, James B; Windham, Michael D; Yatskievych, George; Pryer, Kathleen M
Polyploidy presents a challenge to those wishing to delimit the species within a group and reconstruct the phylogenetic relationships among these taxa. A clear understanding of the tree-like relationships among the diploid species can provide a framework upon which to reconstruct the reticulate events that gave rise to the polyploid lineages. In this study we apply this "diploids-first" strategy to the fern genus Astrolepis (Pteridaceae). Diploids are identified using the number of spores per sporangium and spore size. Analyses of plastid and low-copy nuclear sequence data provide well-supported estimates of phylogenetic relationships, including strong evidence for two morphologically distinctive diploid lineages not recognized in recent treatments. One of these corresponds to the type of Notholaena deltoidea, a species that has not been recognized in any modern treatment of Astrolepis. This species is resurrected here as the new combination Astrolepis deltoidea . The second novel lineage is that of a diploid initially hypothesized to exist by molecular and morphological characteristics of several established Astrolepis allopolyploids. This previously missing diploid species is described here as Astrolepis obscura. © Copyright 2010 by the American Society of Plant Taxonomists.
Open Access
A molecular phylogeny of scaly tree ferns (Cyatheaceae).
(American journal of botany, 2007-05) Korall, P; Conant, DS; Metzgar, JS; Schneider, H; Pryer, KM
Tree ferns recently were identified as the closest sister group to the hyperdiverse clade of ferns, the polypods. Although most of the 600 species of tree ferns are arborescent, the group encompasses a wide range of morphological variability, from diminutive members to the giant scaly tree ferns, Cyatheaceae. This well-known family comprises most of the tree fern diversity (∼500 species) and is widespread in tropical, subtropical, and south temperate regions of the world. Here we investigate the phylogenetic relationships of scaly tree ferns based on DNA sequence data from five plastid regions (rbcL, rbcL-accD IGS, rbcL-atpB IGS, trnG-trnR, and trnL-trnF). A basal dichotomy resolves Sphaeropteris as sister to all other taxa and scale features support these two clades: Sphaeropteris has conform scales, whereas all other taxa have marginate scales. The marginate-scaled clade consists of a basal trichotomy, with the three groups here termed (1) Cyathea (including Cnemidaria, Hymenophyllopsis, Trichipteris), (2) Alsophila sensu stricto, and (3) Gymnosphaera (previously recognized as a section within Alsophila) + A. capensis. Scaly tree ferns display a wide range of indusial structures, and although indusium shape is homoplastic it does contain useful phylogenetic information that supports some of the larger clades recognised.
Open Access
A numerical analysis of chromatographic profiles in North American taxa of the fern genus Gymnocarpium
(Canadian Journal of Botany, 1983-10-01) Pryer, Kathleen M; Britton, Donald M; McNeill, John
As part of a systematic investigation of the genus Gymnocarpium in North America, a survey of chromatographic profiles in species and hybrids of the genus was initiated. It was established through cluster analysis and ordination of the phenolic data that morphologically distinguishable taxa of Gymnocarpium can be recognized by their chromatographic profiles alone. These data provide supportive evidence for the recognition of G. robertianum and G. jessoense ssp. parvulum as distinct taxa and for the hybrid status of G. × intermedium. They also suggest that, as currently circumscribed, G. jessoense ssp. jessoense is a heterogeneous taxon.
Open Access
A plastid phylogeny of the cosmopolitan fern family cystopteridaceae (Polypodiopsida)
(Systematic Botany, 2013-06-01) Rothfels, CJ; Windham, MD; Pryer, KM
Among the novel results of recent molecular phylogenetic analyses are the unexpectedly close evolutionary relationships of the genera Acystopteris, Cystopteris, and Gymnocarpium, and the phylogenetic isolation of these genera from Woodsia. As a consequence, these three genera have been removed from Woodsiaceae and placed into their own family, the Cystopteridaceae. Despite the ubiquity of this family in rocky habitats across the northern hemisphere, and its cosmopolitan distribution (occurring on every continent except Antarctica), sampling of the Cystopteridaceae in phylogenetic studies to date has been sparse. Here we assemble a three-locus plastid dataset (matK, rbcL, trnG-R) that includes most recognized species in the family and multiple accessions of widespread taxa from across their geographic ranges. All three sampled genera are robustly supported as monophyletic, Cystopteris is strongly supported as sister to Acystopteris, and those two genera together are sister to Gymnocarpium. The Gymnocarpium phylogeny is deeply divided into three major clades, which we label the disjunctum clade, the robertianum clade, and core Gymnocarpium. The Cystopteris phylogeny, similarly, features four deeply diverged clades: C. montana, the sudetica clade, the bulbifera clade, and the fragilis complex. Acystopteris includes only three species, each of which is supported as monophyletic, with A. taiwaniana sister to the japonica/tenuisecta clade. Our results yield the first species-level phylogeny of the Cystopteridaceae and the first molecular phylogenetic evidence for species boundaries. These data provide an essential foundation for further investigations of complex patterns of geographic diversification, speciation, and reticulation in this family. © Copyright 2013 by the American Society of Plant Taxonomists.
Open Access
A revised family-level classification for eupolypod II ferns (Polypodiidae: Polypodiales)
(Taxon, 2012-01-01) Rothfels, CJ; Sundue, MA; Kuo, L; Larsson, A; Kato, M; Schuettpelz, E; Pryer, KM
We present a family-level classification for the eupolypod II clade of leptosporangiate ferns, one of the two major lineages within the Eupolypods, and one of the few parts of the fern tree of life where family-level relationships were not well understood at the time of publication of the 2006 fern classification by Smith & al. Comprising over 2500 species, the composition and particularly the relationships among the major clades of this group have historically been contentious and defied phylogenetic resolution until very recently. Our classification reflects the most current available data, largely derived from published molecular phylogenetic studies. In comparison with the five-family (Aspleniaceae, Blechnaceae, Onocleaceae, Thelypteridaceae, Woodsiaceae) treatment of Smith & al., we recognize 10 families within the eupolypod II clade. Of these, Aspleniaceae, Thelypteridaceae, Blechnaceae, and Onocleaceae have the same composition as treated by Smith & al. Woodsiaceae, which Smith & al. acknowledged as possibly non-monophyletic in their treatment, is circumscribed here to include only Woodsia and its segregates; the other "woodsioid" taxa are divided among Athyriaceae, Cystopteridaceae, Diplaziopsidaceae, Rhachidosoraceae, and Hemidictyaceae. We provide circumscriptions for each family, which summarize their morphological, geographical, and ecological characters, as well as a dichotomous key to the eupolypod II families. Three of these families- Diplaziopsidaceae, Hemidictyaceae, and Rhachidosoraceae-were described in the past year based on molecular phylogenetic analyses; we provide here their first morphological treatment.
Open Access
A revised generic classification of vittarioid ferns (Pteridaceae) based on molecular, micromorphological, and geographic data
(Taxon, 2016-08-01) Schuettpelz, E; Chen, C; Kessler, M; Pinson, JB; Johnson, G; Davila, A; Cochran, AT; Huiet, L; Pryer, KM
© International Association for Plant Taxonomy (IAPT) 2016. Vittarioid ferns compose a well-supported clade of 100-130 species of highly simplified epiphytes in the family Pteridaceae. Generic circumscriptions within the vittarioid clade were among the first in ferns to be evaluated and revised based on molecular phylogenetic data. Initial analyses of rbcL sequences revealed strong geographic structure and demonstrated that the two largest vittarioid genera, as then defined, each had phylogenetically distinct American and Old World components. The results of subsequent studies that included as many as 36 individuals of 33 species, but still relied on a single gene, were generally consistent with the early findings. Here, we build upon the previous datasets, incorporating many more samples (138 individuals representing 72 species) and additional plastid markers (atpA, chlN, rbcL, rpoA). Analysis of our larger dataset serves to better characterize known lineages, reveals new lineages, and ultimately uncovers an underlying geographic signal that is even stronger than was previously appreciated. In our revised generic classification, we recognize a total of eleven vittarioid genera. Each genus, including the new genus Antrophyopsis (Benedict) Schuettp., stat. nov., is readily diagnosable based on morphology, with micromorphological characters related to soral paraphyses and spores complementing more obvious features such as venation and the distribution of sporangia. A key to the currently recognized vittarioid genera, brief generic descriptions, and five new species combinations are provided.
Open Access
A synopsis of the genus Sanicula (Apiaceae) in eastern Canada
(Canadian Journal of Botany, 1989-01-01) Pryer, KM; Phillippe, LR
Four species and 2 varieties of these native woodland umbellifers are recognized. A key to the taxa, comparative descriptions of diagnostic characters, and notes on the taxonomy, distribution, habitat, and rare status are provided. Eastern Canadian dot maps and North American range maps are included for each taxon. -from Authors
Open Access
A worldwide phylogeny of Adiantum (Pteridaceae) reveals remarkable convergent evolution in leaf blade architecture
(Taxon, 2018-06-01) Huiet, L; Li, F; Kao, T; Prado, J; Smith, AR; Schuettpelz, E; Pryeri, KM
© International Association for Plant Taxonomy (IAPT) 2018, All rights reserved. Adiantum is among the most distinctive and easily recognized leptosporangiate fern genera. Despite encompassing an astonishing range of leaf complexity, all species of Adiantum share a unique character state not observed in other ferns: sporangia borne directly on the reflexed leaf margin or “false indusium” (pseudoindusium). The over 200 species of Adiantum span six continents and are nearly all terrestrial. Here, we present one of the most comprehensive phylogenies for any large (200+ spp.) monophyletic, subcosmopolitan genus of ferns to date. We build upon previous datasets, providing new data from four plastid markers (rbcL, atpA, rpoA, chlN) for 146 taxa. All sampled taxa can be unequivocally assigned to one of nine robustly supported clades. Although some of these unite to form larger, well-supported lineages, the backbone of our phylogeny has several short branches and generally weak support, making it difficult to accurately assess deep relationships. Our maximum likelihood-based ancestral character state reconstructions of leaf blade architecture reveal remarkable convergent evolution across multiple clades for nearly all leaf forms. A single unique synapomorphy—leaves once-pinnate, usually with prolonged rooting tips—defines the philippense clade. Although a rare occurrence in Adiantum, simple leaves occur in three distinct clades (davidii, philippense, peruvianum). Most taxa have leaves that are more than once-pinnate, and only a few of these (in the formosum and pedatum clades) exhibit the distinct pseudopedate form. Distributional ranges for each of the terminal taxa show that most species (75%) are restricted to only one of six major biogeographical regions. Forty-eight of our sampled species (nearly one-third) are endemic to South America.
Open Access
Are there too many fern genera?
(Taxon, 2018-06-01) Schuettpelz, E; Rouhan, G; Pryer, KM; Rothfels, CJ; Prado, J; Sundue, MA; Windham, MD; Moran, RC; Smith, AR
Open Access
Assessing phylogenetic relationships in extant heterosporous ferns (Salviniales), with a focus on Pilularia and Salvinia
(Botanical Journal of the Linnean Society, 2008-08-01) Nagalingum, NS; Nowak, MD; Pryer, KM
Heterosporous ferns (Salviniales) are a group of approximately 70 species that produce two types of spores (megaspores and microspores). Earlier broad-scale phylogenetic studies on the order typically focused on one or, at most, two species per genus. In contrast, our study samples numerous species for each genus, wherever possible, accounting for almost half of the species diversity of the order. Our analyses resolve Marsileaceae, Salviniaceae and all of the component genera as monophyletic. Salviniaceae incorporate Salvinia and Azolla; in Marsileaceae, Marsilea is sister to the clade of Regnellidium and Pilularia - this latter clade is consistently resolved, but not always strongly supported. Our individual species-level investigations for Pilularia and Salvinia, together with previously published studies on Marsilea and Azolla (Regnellidium is monotypic), provide phylogenies within all genera of heterosporous ferns. The Pilularia phylogeny reveals two groups: Group I includes the European taxa P. globulifera and P. minuta; Group II consists of P. americana, P. novae-hollandiae and P. novae-zelandiae from North America, Australia and New Zealand, respectively, and are morphologically difficult to distinguish. Based on their identical molecular sequences and morphology, we regard P. novae-hollandiae and P. novae-zelandiae to be conspecific; the name P. novae-hollandiae has nomenclatural priority. The status of P. americana requires further investigation as it consists of two geographically and genetically distinct North American groups and also shows a high degree of sequence similarity to P. novae-hollandiae. Salvinia also comprises biogeographically distinct units - a Eurasian group (S. natans and S. cucullata) and an American clade that includes the noxious weed S. molesta, as well as S. oblongifolia and S. minima. © 2008 The Linnean Society of London.
Open Access
Baja: A New Monospecific Genus Segregated from Cheilanthes s. l. (Pteridaceae)
(Systematic Botany, 2019-09-06) George, LO; Pryer, KM; Kao, T; Huiet, L; Windham, MD
Open Access
Comparative morphology of reproductive structures in heterosporous water ferns and a reevaluation of the sporocarp
(International Journal of Plant Sciences, 2006-07-01) Nagalingum, NS; Schneider, H; Pryer, KM
Heterosporous water ferns (Marsileaceae and Salviniaceae) are the only extant group of plants to have evolved heterospory since the Paleozoic. These ferns possess unusual reproductive structures traditionally termed "sporocarps." Using an evolutionary framework, we critically examine the complex homology issues pertaining to these structures. Comparative morphological study reveals that all heterosporous ferns bear indusiate sori on a branched, nonlaminate structure that we refer to as the sorophore; this expanded definition highlights homology previously obscured by the use of different terms. By using a homology-based concept, we aim to discontinue the use of historically and functionally based morphological terminology. We recognize the sorophore envelope as a structure that surrounds the sorophore and sori. The sorophore envelope is present in Marsileaceae as a sclerenchymatous sporocarp wall and in Azolla as a parenchymatous layer, but it is absent in Salvinia. Both homology assessments and phylogenetic character-state reconstructions using the Cretaceous fossil Hydropteris are consistent with a single origin of the sorophore envelope in heterosporous ferns. Consequently, we restrict the term "sporocarp" to a sorophore envelope and all it contains. Traditional usage of "sporocarp" is misleading because it implies homology for nonhomologous structures, and structures historically called sporocarps in Salviniaceae are more appropriately referred to as sori. © 2006 by The University of Chicago. All rights reserved.
Open Access
Deciphering the origins of apomictic polyploids in the Cheilanthes yavapensis complex (Pteridaceae).
(American journal of botany, 2009-09) Grusz, AL; Windham, MD; Pryer, KM
Deciphering species relationships and hybrid origins in polyploid agamic species complexes is notoriously difficult. In this study of cheilanthoid ferns, we demonstrate increased resolving power for clarifying the origins of polyploid lineages by integrating evidence from a diverse selection of biosystematic methods. The prevalence of polyploidy, hybridization, and apomixis in ferns suggests that these processes play a significant role in their evolution and diversification. Using a combination of systematic approaches, we investigated the origins of apomictic polyploids belonging to the Cheilanthes yavapensis complex. Spore studies allowed us to assess ploidy levels; plastid and nuclear DNA sequencing revealed evolutionary relationships and confirmed the putative progenitors (both maternal and paternal) of taxa of hybrid origin; enzyme electrophoretic evidence provided information on genome dosage in allopolyploids. We find here that the widespread apomictic triploid, Cheilanthes lindheimeri, is an autopolyploid derived from a rare, previously undetected sexual diploid. The apomictic triploid Cheilanthes wootonii is shown to be an interspecific hybrid between C. fendleri and C. lindheimeri, whereas the apomictic tetraploid C. yavapensis is comprised of two cryptic and geographically distinct lineages. We show that earlier morphology-based hypotheses of species relationships, while not altogether incorrect, only partially explain the complicated evolutionary history of these ferns.
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, 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.
Open Access
Expression level dominance and homeolog expression bias in recurrent origins of the allopolyploid fern polypodium hesperium
(American Fern Journal, 2019-07-01) Sigel, EM; Der, JP; Windham, MD; Pryer, KM
© 2019 American Fern Society. All rights reserved. Allopolyploidization is a common mode of speciation in ferns with many taxa having formed recurrently from distinct hybridization events between the same parent species. Each hybridization event marks the union of divergent parental gene copies, or homeologs, and the formation of an independently derived lineage. Little is known about the effects of recurrent origins on the genomic composition and phenotypic variation of allopolyploid fern taxa. To begin to address this knowledge gap, we investigated gene expression patterns in two naturally formed, independently derived lineages of the allotetraploid fern Polypodium hesperium relative to its diploid progenitor species, Polypodium amorphum and Polypodium glycyrrhiza. Using RNA-sequencing to survey total gene expression levels for 19194 genes and homeolog-specific expression for 1073 genes, we found that, in general, gene expression in both lineages of P. hesperium was biased toward P. amorphum - both by mirroring expression levels of P. amorphum and preferentially expressing homeologs derived from P. amorphum. However, we recovered substantial expression variation between the two lineages at the level of individual genes and among individual specimens. Our results align with similar transcriptome profile studies of angiosperms, suggesting that expression in many allopolyploid plants reflects the dominance of a specific parental subgenome, but that recurrent origins impart substantial expression, or phenotypic, variation to allopolyploid taxa.
Open Access
Fern Phylogeny Based on rbcL Nucleotide Sequences
(American Fern Journal, 1995-10) Hasebe, Mitsuyasu; Wolf, Paul G; Pryer, Kathleen M; Ueda, Kunihiko; Ito, Motomi; Sano, Ryosuke; Gastony, Gerald J; Yokoyama, Jun; Manhart, James R; Murakami, Noriaki; Crane, Edmund H; Haufler, Christopher H; Hauk, Warren D
Open Access
Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes
(Taxon, 2007-01-01) Schuettpelz, E; Pryer, KM
In an effort to obtain a solid and balanced approximation of global fern phylogeny to serve as a tool for addressing large-scale evolutionary questions, we assembled and analyzed the most inclusive molecular dataset for leptosporangiate ferns to date. Three plastid genes (rbcL, atpB, atpA), totaling more than 4,000 bp, were sequenced for each of 400 leptosporangiate fern species (selected using a proportional sampling approach) and five outgroups. Maximum likelihood analysis of these data yielded an especially robust phylogeny: 80% of the nodes were supported by a maximum likelihood bootstrap percentage ≥ 70. The scope of our analysis provides unprecedented insight into overall fern relationships, not only delivering additional support for the deepest leptosporangiate divergences, but also uncovering the composition of more recently emerging clades and their relationships to one another.
Open Access
Game Changer in Soil Science. The Anthropocene in soil science and pedology.
(Journal of Plant Nutrition and Soil Science, 2020-02-01) Richter, DD
© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim The venerable science of pedology, initiated in the 19th century as the study of the natural factors of soil formation, is adapting to the demands of the Anthropocene, the geologic time during which planet Earth and its soils are transitioning from natural to human-natural systems. With vast areas of soils intensively managed, the future of pedology lies with a renewed science that can be called anthropedology that builds on the pedology of the past but proceeds from “human as outsider” to “human as insider.” In other words, the human in pedology must shift from being a soil-disturbing to soil-forming agent. Pedology is well prepared to respond to the challenges of the Anthropocene, given the decades of research on human-soil relations throughout human history and throughout the period of the Great Acceleration (Steffen et al., [76]). However, quantitative understanding of soil responses to the diversity of human forcings remains elementary and needs remedy.
Open Access
Hydrological and ecological responses of ecosystems to extreme precipitation regimes: A test of empirical-based hypotheses with an ecosystem model
(Perspectives in Plant Ecology, Evolution and Systematics, 2016-10-01) Ye, JS; Reynolds, JF; Maestre, FT; Li, FM
Many uncertainties exist in our quest to understand and predict how terrestrial ecosystems will respond to climate change. A particularly challenging issue is how increases in extreme precipitation regimes, which are characterized by larger but fewer individual precipitation events, will impact ecosystems. Based on a wide-ranging review of empirical studies of both hydrological and ecological processes, Knapp et al. (2008) generated a suite of hypotheses positing how these processes would respond to an increase in extreme precipitation regimes and, from this, concluded that mesic ecosystems would be more detrimentally impacted than xeric ones. In this study we present the first thorough test of these hypotheses by examining how forest, shrubland, grassland and desert ecosystems of the Tibetan Plateau, having very different vegetation and climate characteristics, respond to more extreme rainfall regimes. We accomplished this by using a simulation model (Biome-BGC) to examine the integrated behavior of these ecosystems based on the simultaneous responses and interactions of 10 hydrological and ecological processes: runoff, canopy evaporation, soil evaporation, soil water storage, transpiration, net primary productivity, soil respiration, net ecosystem exchange, nitrogen [N] mineralization, and N leaching. We ran forty-year simulations (1986–2008) where we manipulated mean growing season precipitation to create more extreme intra-annual precipitation regimes characterized by lower precipitation frequencies, longer dry periods, and larger individual (daily) precipitation events. When compared to ambient conditions, our simulations showed that increases in extreme rainfall regimes (1) impacted all hydrological processes in mesic ecosystems, resulting in a reduction of soil mineral N due to increased leaching; and (2) enhanced plant growth in xeric ecosystems, leading to larger and denser canopies and higher light interception. The responses of hydrological processes tended to follow Knapp et al.’s hypotheses more so than ecological responses. Overall, responses of mesic ecosystems closely followed the hypotheses but xeric ecosystems were highly variable and only weakly consistent with them. Our findings provide new insights as to how more extreme rainfall regimes may potentially affect the functioning of terrestrial ecosystems.

Browsing by Subject "Plant Sciences"

Results Per Page

Sort Options