Browsing by Author "Pryer, KM"
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Item Open Access A classification for extant ferns(Taxon, 2006-01-01) Smith, AR; Pryer, KM; Schuettpelz, E; Korall, P; Schneider, H; Wolf, PGWe 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.Item Open Access A first glimpse at genes important to the Azolla–Nostoc symbiosis(Symbiosis, 2019-01-01) Eily, AN; Pryer, KM; Li, F© 2019, Springer Nature B.V. Azolla is a small genus of diminutive aquatic ferns with a surprisingly vast potential to benefit the environment and agriculture, as well as to provide insight into the evolution of plant-cyanobacterial symbioses. This capability is derived from the unique relationship Azolla spp. have with their obligate, nitrogen-fixing cyanobacterial symbiont, Nostoc azollae, that resides in their leaves. Although previous work has specified the importance of the exchange of ammonium and sucrose metabolites between these two partners, we have yet to determine the underlying molecular mechanisms that make this symbiosis so successful. The newly sequenced and annotated reference genome of Azolla filiculoides has allowed us to investigate gene expression profiles of A. filiculoides—both with and without its obligate cyanobiont, N. azollae—revealing genes potentially essential to the Azolla-Nostoc symbiosis. We observed the absence of differentially expressed glutamine synthetase (GS) and glutamate synthase (GOGAT) genes, leading to questions about how A. filiculoides regulates the machinery it uses for nitrogen assimilation. Ushering A. filiculoides into the era of transcriptomics sets the stage to truly begin to understand the uniqueness of the Azolla-Nostoc symbiosis.Item 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, KMTree 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.Item Open Access A molecular phylogeny of the fern family Pteridaceae: assessing overall relationships and the affinities of previously unsampled genera.(Molecular phylogenetics and evolution, 2007-09) Schuettpelz, E; Schneider, H; Huiet, L; Windham, MD; Pryer, KMThe monophyletic Pteridaceae accounts for roughly 10% of extant fern diversity and occupies an unusually broad range of ecological niches, including terrestrial, epiphytic, xeric-adapted rupestral, and even aquatic species. In this study, we present the results of the first broad-scale and multi-gene phylogenetic analyses of these ferns, and determine the affinities of several previously unsampled genera. Our analyses of two newly assembled data sets (including 169 newly obtained sequences) resolve five major clades within the Pteridaceae: cryptogrammoids, ceratopteridoids, pteridoids, adiantoids, and cheilanthoids. Although the composition of these clades is in general agreement with earlier phylogenetic studies, it is very much at odds with the most recent subfamilial classification. Of the previously unsampled genera, two (Neurocallis and Ochropteris) are nested within the genus Pteris; two others (Monogramma and Rheopteris) are early diverging vittarioid ferns, with Monogramma resolved as polyphyletic; the last previously unsampled genus (Adiantopsis) occupies a rather derived position among cheilanthoids. Interestingly, some clades resolved within the Pteridaceae can be characterized by their ecological preferences, suggesting that the initial diversification in this family was tied to ecological innovation and specialization. These processes may well be the basis for the diversity and success of the Pteridaceae today.Item Open Access A novel chloroplast gene reported for flagellate plants.(American journal of botany, 2018-01) Song, M; Kuo, L; Huiet, L; Pryer, KM; Rothfels, CJ; Li, FPREMISE OF THE STUDY:Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (ORF) in the fern lineage that is conserved across flagellate plants. METHODS:We initially detected a putative uncharacterized ORF by the existence of a highly conserved region between rps16 and matK in a series of matK alignments of leptosporangiate ferns. We mined available plastid genomes for this ORF, which we now refer to as ycf94, to infer evolutionary selection pressures and assist in functional prediction. To further examine the transcription of ycf94, we assembled the plastid genome and sequenced the transcriptome of the leptosporangiate fern Adiantum shastense Huiet & A.R. Sm. KEY RESULTS:The ycf94 predicted protein has a distinct transmembrane domain but with no sequence homology to other proteins with known function. The nonsynonymous/synonymous substitution rate ratio of ycf94 is on par with other fern plastid protein-encoding genes, and additional homologs can be found in a few lycophyte, moss, hornwort, and liverwort plastid genomes. Homologs of ycf94 were not found in seed plants. In addition, we report a high level of RNA editing for ycf94 transcripts-a hallmark of protein-coding genes in fern plastomes. CONCLUSIONS:The degree of sequence conservation, together with the presence of a distinct transmembrane domain and RNA-editing sites, suggests that ycf94 is a protein-coding gene of functional significance in ferns and, potentially, bryophytes and lycophytes. However, the origin and exact function of this gene require further investigation.Item Open Access A plastid phylogeny of the cosmopolitan fern family cystopteridaceae (Polypodiopsida)(Systematic Botany, 2013-06-01) Rothfels, CJ; Windham, MD; Pryer, KMAmong 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.Item Open Access A revised classification for eupolypod II ferns (Polypodiales: Polypodiopsida)(Taxon, 2012) Rothfels, CJ; Sundue, MA; Kato, M; Larsson, A; Kuo, LY; Schuettpelz, E; Pryer, KMItem 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, KMWe 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.Item 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.Item Open Access A step-by-step protocol for meiotic chromosome counts in flowering plants: A powerful and economical technique revisited.(Applications in plant sciences, 2020-04-23) Windham, MD; Pryer, KM; Poindexter, DB; Li, F; Rothfels, CJ; Beck, JBPremise:Counting chromosomes is a fundamental botanical technique, yet it is often intimidating and increasingly sidestepped. Once mastered, the basic protocol can be applied to a broad range of taxa and research questions. It also reveals an aspect of the plant genome that is accessible with only the most basic of resources-access to a microscope with 1000× magnification is the most limiting factor. Methods and Results:Here we provide a detailed protocol for choosing, staining, and squashing angiosperm pollen mother cells. The protocol is supplemented by figures and two demonstration videos. Conclusions:The protocol we provide will hopefully demystify and reinvigorate a powerful and once commonplace botanical technique that is available to researchers regardless of their location and resources.Item Open Access A synopsis of the genus Sanicula (Apiaceae) in eastern Canada(Canadian Journal of Botany, 1989-01-01) Pryer, KM; Phillippe, LRFour 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 AuthorsItem Open Access A Unified Approach to Taxonomic Delimitation in the Fern Genus Pentagramma (Pteridaceae)(Systematic Botany, 2015-01-01) Schuettpelz, E; Pryer, KM; Windham, MD© Copyright 2015 by the American Society of Plant Taxonomists.The native goldback and silverback ferns of western North America, composing the genus Pentagramma, are phylogenetically isolated within the xeric-adapted cheilanthoid clade. Although species-poor compared to its sister group, Pentagramma encompasses a diverse array of morphotypes, cytotypes, and flavonoid chemotypes. Because the differences are generally cryptic, however, the various entities are usually recognized at an infraspecific level. In recent years, as many as five subspecies have been ascribed to P. triangularis, and only P. pallida has been considered sufficiently divergent to warrant recognition as a distinct species. In this study, we take a unified approach to taxonomic delimitation in Pentagramma. Combining spore studies with phylogenetic analyses of plastid and nuclear sequences, we identify six genetically and morphologically distinct diploid lineages, each of which is here treated as a species. A new species is described (P. glanduloviscida) and three new combinations are made (P. maxonii, P. rebmanii, and P. viscosa).Item Open Access Adiantumshastense, a new species of maidenhair fern from California.(PhytoKeys, 2015) Huiet, L; Lenz, M; Nelson, JK; Pryer, KM; Smith, ARA new species of Adiantum is described from California. This species is endemic to northern California and is currently known only from Shasta County. We describe its discovery after first being collected over a century ago and distinguish it from Adiantumjordanii and Adiantumcapillus-veneris. It is evergreen and is sometimes, but not always, associated with limestone. The range of Adiantumshastense Huiet & A.R.Sm., sp. nov., is similar to several other Shasta County endemics that occur in the mesic forests of the Eastern Klamath Range, close to Shasta Lake, on limestone and metasedimentary substrates.Item Open Access Applying Machine Learning to Investigate Long Term Insect-Plant Interactions Preserved on Digitized Herbarium Specimens(Applications in plant sciences, 2020) Meineke, EK; Tomasi, C; Yuan, S; Pryer, KMAbstractPremise of the studyDespite the economic importance of insect damage to plants, long-term data documenting changes in insect damage (‘herbivory’) and diversity are limited. Millions of pressed plant specimens are now available online for collecting big data on plant-insect interactions during the Anthropocene.MethodsWe initiated development of machine learning methods to automate extraction of herbivory data from herbarium specimens. We trained an insect damage detector and a damage type classifier on two distantly related plant species. We experimented with 1) classifying six types of herbivory and two control categories of undamaged leaf, and 2) detecting two of these damage categories for which several hundred annotations were available.ResultsClassification models identified the correct type of herbivory 81.5% of the time. The damage classifier was accurate for categories with at least one hundred test samples. We show anecdotally that the detector works well when asked to detect two types of damage.DiscussionThe classifier and detector together are a promising first step for the automation of herbivory data collection. We describe ongoing efforts to increase the accuracy of these models to allow other researchers to extract similar data and apply them to address a variety of biological hypotheses.Item 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, ARItem 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, KMHeterosporous 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.Item 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, MDItem 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, KMHeterosporous 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.Item Open Access Crowdfunding the Azolla fern genome project: a grassroots approach(GigaScience, 2014) Li, F; Pryer, KMItem Open Access Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns.(BMC evolutionary biology, 2007-09-08) Haugen, P; Bhattacharya, D; Palmer, JD; Turner, S; Lewis, LA; Pryer, KMGroup I introns are one of the four major classes of introns as defined by their distinct splicing mechanisms. Because they catalyze their own removal from precursor transcripts, group I introns are referred to as autocatalytic introns. Group I introns are common in fungal and protist nuclear ribosomal RNA genes and in organellar genomes. In contrast, they are rare in all other organisms and genomes, including bacteria.Here we report five group I introns, each containing a LAGLIDADG homing endonuclease gene (HEG), in large subunit (LSU) rRNA genes of cyanobacteria. Three of the introns are located in the LSU gene of Synechococcus sp. C9, and the other two are in the LSU gene of Synechococcus lividus strain C1. Phylogenetic analyses show that these introns and their HEGs are closely related to introns and HEGs located at homologous insertion sites in organellar and bacterial rDNA genes. We also present a compilation of group I introns with homing endonuclease genes in bacteria.We have discovered multiple HEG-containing group I introns in a single bacterial gene. To our knowledge, these are the first cases of multiple group I introns in the same bacterial gene (multiple group I introns have been reported in at least one phage gene and one prophage gene). The HEGs each contain one copy of the LAGLIDADG motif and presumably function as homodimers. Phylogenetic analysis, in conjunction with their patchy taxonomic distribution, suggests that these intron-HEG elements have been transferred horizontally among organelles and bacteria. However, the mode of transfer and the nature of the biological connections among the intron-containing organisms are unknown.