Browsing by Author "Huiet, L"
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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 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 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 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 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 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 Patterns of diversification in the xeric-adapted fern genus myriopteris (Pteridaceae)(Systematic Botany, 2014-01-01) Grusz, AL; Windham, MD; Yatskievych, G; Huiet, L; Gastony, GJ; Pryer, KMStrong selective pressures imposed by drought-prone habitats have contributed to extensive morphological convergence among the 400 + species of cheilanthoid ferns (Pteridaceae). As a result, generic circumscriptions based exclusively on macromorphology often prove to be non-monophyletic. Ongoing molecular phylogenetic analyses are providing the foundation for a revised classification of this challenging group and have begun to clarify its complex evolutionary history. As part of this effort, we generated and analyzed DNA sequence data for three plastid loci (rbcL, atpA, and the intergenic spacer trnG-trnR) for the myriopterid clade, one of the largest monophyletic groups of cheilanthoid ferns. This lineage encompasses 47 primarily North and Central American taxa previously included in Cheilanthes but now placed in the recircumscribed genus Myriopteris. Here, we infer a phylogeny for the group and examine key morphological characters across this phylogeny. We also include a brief discussion of the three well-supported Myriopteris subclades, along with a review of reproductive mode and known ploidy levels for members of this early diverging lineage of cheilanthoid ferns. © Copyright 2014 by the American Society of Plant Taxonomists.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 Species relationships and farina evolution in the cheilanthoid fern genus Argyrochosma (Pteridaceae)(Systematic Botany, 2011-07-01) Sigel, EM; Windham, MD; Huiet, L; Yatskievych, G; Pryer, KMConvergent evolution driven by adaptation to arid habitats has made it difficult to identify monophyletic taxa in the cheilanthoid ferns. Dependence on distinctive, but potentially homoplastic characters, to define major clades has resulted in a taxonomic conundrum: all of the largest cheilanthoid genera have been shown to be polyphyletic. Here we reconstruct the first comprehensive phylogeny of the strictly New World cheilanthoid genus Argyrochosma. We use our reconstruction to examine the evolution of farina (powdery leaf deposits), which has played a prominent role in the circumscription of cheilanthoid genera. Our data indicate that Argyrochosma comprises two major monophyletic groups: one exclusively non-farinose and the other primarily farinose. Within the latter group, there has been at least one evolutionary reversal (loss) of farina and the development of major chemical variants that characterize specific clades. Our phylogenetic hypothesis, in combination with spore data and chromosome counts, also provides a critical context for addressing the prevalence of polyploidy and apomixis within the genus. Evidence from these datasets provides testable hypotheses regarding reticulate evolution and suggests the presence of several previously undetected taxa of Argyrochosma. © 2011 by the American Society of Plant Taxonomists.Item Open Access The evolutionary history of ferns inferred from 25 low-copy nuclear genes.(Am J Bot, 2015-07) Rothfels, CJ; Li, F; Sigel, EM; Huiet, L; Larsson, A; Burge, DO; Ruhsam, M; Deyholos, M; Soltis, DE; Stewart Jr, CNUNLABELLED: • PREMISE OF THE STUDY: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.Item Open Access Transcriptome-mining for single-copy nuclear markers in ferns.(PloS one, 2013-01) Rothfels, CJ; Larsson, A; Li, F; Sigel, EM; Huiet, L; Burge, DO; Ruhsam, M; Graham, SW; Stevenson, DW; Wong, GKBACKGROUND:Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales. PRINCIPAL FINDINGS:We present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs-curated broadly across ferns-that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group. CONCLUSIONS:The 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.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