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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 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 Analysis of enriched rare variants in JPH2-encoded junctophilin-2 among Greater Middle Eastern individuals reveals a novel homozygous variant associated with neonatal dilated cardiomyopathy.(Scientific reports, 2019-06-21) Jones, Edward G; Mazaheri, Neda; Maroofian, Reza; Zamani, Mina; Seifi, Tahereh; Sedaghat, Alireza; Shariati, Gholamreza; Jamshidi, Yalda; Allen, Hugh D; Wehrens, Xander HT; Galehdari, Hamid; Landstrom, Andrew PJunctophilin-2 (JPH2) is a part of the junctional membrane complex that facilitates calcium-handling in the cardiomyocyte. Previously, missense variants in JPH2 have been linked to hypertrophic cardiomyopathy; however, pathogenic "loss of function" (LOF) variants have not been described. Family-based genetic analysis of GME individuals with cardiomyopathic disease identified an Iranian patient with dilated cardiomyopathy (DCM) as a carrier of a novel, homozygous single nucleotide insertion in JPH2 resulting in a stop codon (JPH2-p.E641*). A second Iranian family with consanguineous parents hosting an identical heterozygous variant had 2 children die in childhood from cardiac failure. To characterize ethnicity-dependent genetic variability in JPH2 and to identify homozygous JPH2 variants associated with cardiac disease, we identified variants in JPH2 in a worldwide control cohort (gnomAD) and 2 similar cohorts from the Greater Middle East (GME Variome, Iranome). These were compared against ethnicity-matched clinical whole exome sequencing (WES) referral tests and a case cohort of individuals with hypertrophic cardiomyopathy (HCM) based on comprehensive review of the literature. Worldwide, 1.45% of healthy individuals hosted a rare JPH2 variant with a significantly higher proportion among GME individuals (4.45%); LOF variants were rare overall (0.04%) yet were most prevalent in GME (0.21%). The increased prevalence of LOF variants in GME individuals was corroborated among region-specific, clinical WES cohorts. In conclusion, we report ethnic-specific differences in JPH2 rare variants, with GME individuals being at higher risk of hosting homozygous LOF variants. This conclusion is supported by the identification of a novel JPH2 LOF variant confirmed by segregation analysis resulting in autosomal recessive pediatric DCM due to presumptive JPH2 truncation.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 Distributed solar photovoltaic array location and extent dataset for remote sensing object identification.(Scientific data, 2016-12) Bradbury, Kyle; Saboo, Raghav; L Johnson, Timothy; Malof, Jordan M; Devarajan, Arjun; Zhang, Wuming; M Collins, Leslie; G Newell, RichardEarth-observing remote sensing data, including aerial photography and satellite imagery, offer a snapshot of the world from which we can learn about the state of natural resources and the built environment. The components of energy systems that are visible from above can be automatically assessed with these remote sensing data when processed with machine learning methods. Here, we focus on the information gap in distributed solar photovoltaic (PV) arrays, of which there is limited public data on solar PV deployments at small geographic scales. We created a dataset of solar PV arrays to initiate and develop the process of automatically identifying solar PV locations using remote sensing imagery. This dataset contains the geospatial coordinates and border vertices for over 19,000 solar panels across 601 high-resolution images from four cities in California. Dataset applications include training object detection and other machine learning algorithms that use remote sensing imagery, developing specific algorithms for predictive detection of distributed PV systems, estimating installed PV capacity, and analysis of the socioeconomic correlates of PV deployment.Item 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.Item Open Access Incidence, Characteristics, and Outcomes of Myocardial Infarction in Patients With Peripheral Artery Disease: Insights From the EUCLID Trial.(JAMA cardiology, 2019-01) Olivier, Christoph B; Mulder, Hillary; Hiatt, William R; Jones, W Schuyler; Fowkes, F Gerry R; Rockhold, Frank W; Berger, Jeffrey S; Baumgartner, Iris; Held, Peter; Katona, Brian G; Norgren, Lars; Blomster, Juuso; Patel, Manesh R; Mahaffey, Kenneth WImportance:Patients with peripheral artery disease (PAD) are at high risk for myocardial infarction (MI). Objective:To characterize the incidence and types of MI in a PAD population, identify factors associated with MI, and determine the association of MI with cardiovascular mortality and acute limb ischemia. Design, Setting, and Participants:The Study Comparing Cardiovascular Effects of Ticagrelor and Clopidogrel in Patients With Peripheral Artery Disease (EUCLID) was a double-blind randomized clinical trial conducted at 811 sites in 28 countries that randomized 13 885 patients with symptomatic PAD to monotherapy with ticagrelor or clopidogrel. Participants had an ankle-brachial index (ABI) of 0.80 or less or previous lower extremity revascularization. Median follow-up was 30 months. For these analyses, patients were evaluated for MI occurrence during follow-up irrespective of treatment. Data were analyzed from June 2017 to September 2018. Main Outcomes and Measures:An adjudication clinical events committee classified MI as type 1 (spontaneous), type 2 (secondary), type 3 (sudden cardiac death), type 4a (less than 48 hours after percutaneous coronary intervention), type 4b (definite stent thrombosis), or type 5 (less than 72 hours after coronary artery bypass graft). A multivariate regression model was developed by stepwise selection to identify factors associated with MI, and a time-dependent multivariate Cox regression analysis was performed to determine the association of MI with cardiovascular death and acute limb ischemia requiring hospitalization. Results:Of the 13 885 patients included in this analysis, 9997 (72.0%) were male, and the median (interquartile range) age was 66 (60-73) years. Myocardial infarction occurred in 683 patients (4.9%; 2.4 events per 100 patient-years) during a median follow-up of 30 months. Patients experiencing MI were older (median [interquartile range] age, 69 [62-75] vs 66 [60-72] years), more likely to have diabetes (349 of 683 [51.1%] vs 4996 of 13 202 [37.8%]) or a previous lower extremity revascularization (466 of 683 [68.2%] vs 7409 of 13 202 [56.1%]), and had a lower ABI (if included by ABI) compared with censored patients. Of the 683 patients with MI during follow-up, the most common MI type was type 1 (405 [59.3%]), followed by type 2 (236 [34.6%]), type 4a (14 [2.0%]), type 3 (12 [1.8%]), type 4b (11 [1.6%]), and type 5 (5 [0.7%]). Postrandomization MI was independently associated with cardiovascular death (adjusted hazard ratio, 9.0; 95% CI, 7.3-11.2; P < .001) and acute limb ischemia requiring hospitalization (adjusted hazard ratio, 2.5; 95% CI, 1.3-5.0; P = .008). Conclusions and Relevance:Approximately 5% of patients with symptomatic PAD had an MI during a median follow-up of 30 months. Type 1 MI (spontaneous) was the most common MI type; however, one-third of MIs were type 2 MI (secondary). More research is needed to identify therapies to reduce the risk of MI in patients with PAD and to improve management of type 2 MI. Trial Registration:ClinicalTrials.gov Identifier: NCT01732822.Item Unknown Phylogeny and divergence time estimates for the fern genus Azolla (Salviniaceae)(International Journal of Plant Sciences, 2007-10-22) Metzgar, JS; Schneider, H; Pryer, KMA phylogeny for all extant species of the heterosporous fern genus Azolla is presented here based on more than 5000 base pairs of DNA sequence data from six plastid loci (rbcL, atpB, rps4, trnL-trnF, trnG-trnR, and rps4-trnS). Our results are in agreement with other recent molecular phylogenetic hypotheses that support the monophyly of sections Azolla and Rhizosperma and the proposed relationships within section Azolla. Divergence times are estimated within Azolla using a penalized likelihood approach, integrating data from fossils and DNA sequences. Penalized likelihood analyses estimate a divergence time of 50.7 Ma (Eocene) for the split between sections Azolla and Rhizosperma, 32.5 Ma (Oligocene) for the divergence of Azolla nilotica from A. pinnata within section Rhizosperma, and 16.3 Ma (Miocene) for the divergence of the two lineages within section Azolla (the A. filiculoides + A. rubra lineage from the A. caroliniana + A. microphylla + A. mexicana complex). © 2007 by The University of Chicago. All rights reserved.Item Unknown 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).