Browsing by Author "Schuettpelz, E"
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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 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 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 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 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.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 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 Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy.(Proceedings of the National Academy of Sciences of the United States of America, 2009-07) Schuettpelz, E; Pryer, KMIn today's angiosperm-dominated terrestrial ecosystems, leptosporangiate ferns are truly exceptional--accounting for 80% of the approximately 11,000 nonflowering vascular plant species. Recent studies have shown that this remarkable diversity is mostly the result of a major leptosporangiate radiation beginning in the Cretaceous, following the rise of angiosperms. This pattern is suggestive of an ecological opportunistic response, with the proliferation of flowering plants across the landscape resulting in the formation of many new niches--both on forest floors and within forest canopies--into which leptosporangiate ferns could diversify. At present, one-third of leptosporangiate species grow as epiphytes in the canopies of angiosperm-dominated tropical rain forests. However, we know too little about the evolutionary history of epiphytic ferns to assess whether or not their diversification was in fact linked to the establishment of these forests, as would be predicted by the ecological opportunistic response hypothesis. Here we provide new insight into leptosporangiate diversification and the evolution of epiphytism by integrating a 400-taxon molecular dataset with an expanded set of fossil age constraints. We find evidence for a burst of fern diversification in the Cenozoic, apparently driven by the evolution of epiphytism. Whether this explosive radiation was triggered simply by the establishment of modern angiosperm-dominated tropical rain forest canopies, or spurred on by some other large-scale extrinsic factor (e.g., climate change) remains to be determined. In either case, it is clear that in both the Cretaceous and Cenozoic, leptosporangiate ferns were adept at exploiting newly created niches in angiosperm-dominated ecosystems.Item Open Access Fern phylogeny(2008-01-01) Schuettpelz, E; Pryer, KM© Cambridge University Press 2008 and Cambridge University Press 2009. Introduction As a consequence of employing DNA sequence data and phylogenetic approaches, unprecedented progress has been made in recent years toward a full understanding of the fern tree of life. At the broadest level, molecular phylogenetic analyses have helped to elucidate which of the so-called “fern allies” are indeed ferns, and which are only distantly related (Nickrent et al., 2000; Pryer et al., 2001a; Wikström and Pryer, 2005; Qiu et al., 2006). Slightly more focused analyses have revealed the composition of, and relationships among, the major extant fern clades (Hasebe et al., 1995; Wolf, 1997; Pryer et al., 2004b; Schneider et al., 2004c; Schuettpelz et al., 2006; Schuettpelz and Pryer, 2007). A plethora of analyses, at an even finer scale, has uncovered some of the most detailed associations (numerous references cited below). Together, these studies have helped to answer many long-standing questions in fern systematics. In this chapter, a brief synopsis of vascular plant relationships - as currently understood - is initially provided to place ferns within a broader phylogenetic framework. This is followed by an overview of fern phylogeny, with most attention devoted to the leptosporangiate clade that accounts for the bulk of extant fern diversity. Discussion of finer scale relationships is generally avoided; instead, the reader is directed to the relevant literature, where more detailed information can be found.Item Open Access Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes(Taxon, 2007-01-01) Schuettpelz, E; Pryer, KMIn 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.Item Open Access Maidenhair ferns, adiantum, are indeed monophyletic and sister to shoestring ferns, vittarioids (Pteridaceae)(Systematic Botany, 2016-01-01) Pryer, KM; Huiet, L; Li, F; Rothfels, CJ; Schuettpelz, E© 2016 by the American Society of Plant Taxonomists. Across the tree of life, molecular phylogenetic studies often reveal surprising relationships between taxa with radically different morphologies that have long obscured their close affiliations. A spectacular botanical example is Rafflesia, a holoparasite that produces the largest flowers in the world, but that evolved from tiny-flowered ancestors within the Euphorbiaceae. Outside of parasitic lineages, such abrupt transformations are rarely seen. One exception involves the "maidenhair ferns" (Adiantum), which are quintessential ferns: beautifully dissected, terrestrial, and shade loving. The closely related "shoestring ferns" (vittarioids), in contrast, have an extremely simplified morphology, are canopy-dwelling epiphytes, and exhibit greatly accelerated rates of molecular evolution. While Adiantum and the vittarioids together have been shown to form a robust monophyletic group (adiantoids), there remain unanswered questions regarding the monophyly of Adiantum and the evolutionary history of the vittarioids. Here we review recent phylogenetic evidence suggesting support for the monophyly of Adiantum, and analyze new plastid data to confirm this result. We find that Adiantum is monophyletic and sister to the vittarioids. With this robust phylogenetic framework established for the broadest relationships in the adiantoid clade, we can now focus on understanding the evolutionary processes associated with the extreme morphological, ecological, and genetic transitions that took place within this lineage.Item Open Access Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales).(Frontiers in plant science, 2018-01) Sigel, EM; Schuettpelz, E; Pryer, KM; Der, JPFerns are unique among land plants in having sporophyte and gametophyte phases that are both free living and fully independent. Here, we examine patterns of sporophytic and gametophytic gene expression in the fern Polypodium amorphum, a member of the homosporous polypod lineage that comprises 80% of extant fern diversity, to assess how expression of a common genome is partitioned between two morphologically, ecologically, and nutritionally independent phases. Using RNA-sequencing, we generated transcriptome profiles for three replicates of paired samples of sporophyte leaf tissue and whole gametophytes to identify genes with significant differences in expression between the two phases. We found a nearly 90% overlap in the identity and expression levels of the genes expressed in both sporophytes and gametophytes, with less than 3% of genes uniquely expressed in either phase. We compare our results to those from similar studies to establish how phase-specific gene expression varies among major land plant lineages. Notably, despite having greater similarity in the identity of gene families shared between P. amorphum and angiosperms, P. amorphum has phase-specific gene expression profiles that are more like bryophytes and lycophytes than seed plants. Our findings suggest that shared patterns of phase-specific gene expression among seed-free plants likely reflect having relatively large, photosynthetic gametophytes (compared to the gametophytes of seed plants that are highly reduced). Phylogenetic analyses were used to further investigate the evolution of phase-specific expression for the phototropin, terpene synthase, and MADS-box gene families.Item Open Access Phylogeny and relationships of the neotropical Adiantum raddianum group (Pteridaceae)(Taxon, 2016-12-01) Hirai, RY; Schuettpelz, E; Huiet, L; Pryer, KM; Smith, AR; Prado, J© International Association for Plant Taxonomy (IAPT) 2016. With more than 200 species, the maidenhair fern genus Adiantum is among the top ten most diverse fern genera. Adiantum is pantropical in distribution and, due to the presence of a unique synapomorphy (sporangia borne on indusia rather than laminae), perhaps the most easily recognized fern genus. Many of its members, including numerous cultivars derived from A. raddianum, are grown as ornamentals. Because of its size, a comprehensive taxonomic study of Adiantum is difficult and the genus is perhaps better approached through a series of narrower studies. Here, we focus specifically on A. raddianum and putative allies. We find a newly defined A. raddianum group to be strongly supported as monophyletic and segregated from other maidenhair ferns on the basis of genetic as well as morphological characteristics. Bayesian inference and maximum likelihood analyses of plastid atpA, chlL, chlN, rbcL, and rpoA sequences support the A raddianum clade as sister to A poiretii and its allies. We identify round-reniform indusia to be a characteristic of the A.raddianum group (vs. lunate in the A.poiretii group). Additionally, we find species in the Apoiretii group to differ in having a unique 66 nucleotide deletion in our chlN gene alignment. The neotropical Araddianum group comprises at least 17 species (14 studied here), some widely distributed; one was recently described (A. alan-smithii).Item Open Access Plastid atpA data provide improved support for deep relationships among ferns(Taxon, 2006-01-01) Schuettpelz, E; Korall, P; Pryer, KMDNA sequence data and phylogenetic approaches have contributed greatly to our understanding of fern relationships. Nonetheless, the datasets analyzed to date have not been sufficient to definitively resolve all parts of the global fern phylogeny; additional data and more extensive sampling are necessary. Here, we explore the phylogenetic utility of the plastid atpA gene. Using newly designed primers, we obtained atpA sequences for 52 fern and 6 outgroup taxa, and then evaluated the capabilities of atpA relative to four other molecular markers, as well as the contributions of atpA in combined analyses. The five single-gene datasets differed markedly in the number of variable characters they possessed; and although the relationships resolved in analyses of these datasets were largely congruent, the robustness of the hypotheses varied considerably. The atpA dataset had more variable characters and resulted in a more robustly supported phylogeny than any of the other single gene datasets examined, suggesting that atpA will be exceptionally useful in more extensive studies of fern phylogeny and perhaps also in studies of other plant lineages. When the atpA data were analyzed in combination with the other four markers, an especially robust hypothesis of fern relationships emerged. With the addition of the atpA data, support increased substantially at several nodes; three nodes, which were not well-supported previously, received both good posterior probability and good bootstrap support in the combined 5-gene (> 6 kb) analyses.Item Open Access Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns.(Systematic biology, 2006-06) Schuettpelz, E; Pryer, KMThe rate of molecular evolution is not constant across the Tree of Life. Characterizing rate discrepancies and evaluating the relative roles of time and rate along branches through the past are both critical to a full understanding of evolutionary history. In this study, we explore the interactions of time and rate in filmy ferns (Hymenophyllaceae), a lineage with extreme branch length differences between the two major clades. We test for the presence of significant rate discrepancies within and between these clades, and we separate time and rate across the filmy fern phylogeny to simultaneously yield an evolutionary time scale of filmy fern diversification and reconstructions of ancestral rates of molecular evolution. Our results indicate that the branch length disparity observed between the major lineages of filmy ferns is indeed due to a significant difference in molecular evolutionary rate. The estimation of divergence times reveals that the timing of crown group diversification was not concurrent for the two lineages, and the reconstruction of ancestral rates of molecular evolution points to a substantial rate deceleration in one of the clades. Further analysis suggests that this may be due to a genome-wide deceleration in the rate of nucleotide substitution.Item Open Access Sex and the Single Gametophyte: Revising the Homosporous Vascular Plant Life Cycle in Light of Contemporary Research(BIOSCIENCE, 2016-11) Haufler, CH; Pryer, KM; Schuettpelz, E; Sessa, EB; Farrar, DR; Moran, R; Schneller, JJ; Watkins Jr, JE; Windham, MDItem Open Access The utility of nuclear gapCp in resolving polyploid fern origins(Systematic Botany, 2008-10-01) Schuettpelz, E; Grusz, AL; Windham, MD; Pryer, KMAlthough polyploidy is rampant in ferns and plays a major role in shaping their diversity, the evolutionary history of many polyploid species remains poorly understood. Nuclear DNA sequences can provide valuable information for identifying polyploid origins; however, remarkably few nuclear markers have been developed specifically for ferns, and previously published primer sets do not work well in many fern lineages. In this study, we present new primer sequences for the amplification of a portion of the nuclear gapCp gene (encoding a glyceraldehyde-3-phosphate dehydrogenase). Through a broad survey across ferns, we demonstrate that these primers are nearly universal for this clade. With a case study in cheilanthoids, we show that this rapidly evolving marker is a powerful tool for discriminating between autopolyploids and allopolyploids. Our results indicate that gapCp holds considerable potential for addressing species-level questions across the fern tree of life. © Copyright 2008 by the American Society of Plant Taxonomists.Item Open Access Using Plastid and Nuclear DNA Sequences to Redraw Generic Boundaries and Demystif Species Complexes in Cheilanthoid Ferns.(AMERICAN FERN JOURNAL, 2009-04-01) Windham, MD; Huiet, L; Schuettpelz, E; Grusz, AL; Rothfels, C; Beck, J; Yatskievych, G; Pryer, KM