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| 1 | Chloroplast phylogenomics of the New World grape species (Vitis, Vitaceae)显示文摘Vitis L。(葡萄类) 是经济地很重要的水果庄稼,葡萄和酒的来源。在类以内的种系发生的关系是高度争论的。此处,我们从整个 plastomes 采用顺序数据试图提高 Vitis 种系发生的分辨率。结果作为 monophyletic 支持新世界 Vitis 亚属 Vitis。在 clade 以内, V。californica 是到仍然保持新的姐妹世界 Vitis 亚属 Vitis。在亚属 Vitis 以内,而且,欧亚的 clade 要用体力地被支持并且是到新世界 clade 的姐妹。Vitis vinifera ssp 的 clade。vinifera 和 V。vinifera ssp。sylvestris 是到 Vitis 的核心亚洲人 clade 的姐妹。在北美洲的几普遍的种被发现例如,是在 plastome 树上的 nonmonophyletic 广泛地定义的 Vitis cinerea 和 V。aestivalis 各个需要被分成几种。可能也 nonmonophyly 某种类由于在北美的 Vitis 的杂交的普通出现。由进九个系列的 Munson 的北美的 Vitis 的分类基于种系发生的结果被讨论。分叉时间和系多样化的分析在在晚第三纪开始的北美洲支持 Vitis 的快速的放射。 | Jun Went AJ Harris Yash Kalburgi Ning Zhang Yuan Xu Wei Zheng Stefanie M. Ickert-Bondt Gabriel Johnson Elizabeth A. Zimmer | 2018 | Journal of Systematics and Evolution2018，56，4： | 14 |
| 2 | Phylogenomic analyses of the Photinia complex support the recognition of a new genus Phippsiomeles and the resurrection of a redefined Stranvaesia in Maleae (Rosaceae)显示文摘Photinia and its morphologically similar allies in Maleae(Rosaceae)consist of five currently recognized genera:Aronia,Heteromeles,Photinia,Pourthiaea,and Stranvaesia,and 68 species,distributed in Asia and North and Central America.Despite previous efforts to clarify relationships in this group,the generic delimitations have remained uncertain.Our goals were to reconstruct a robust phylogeny of Photinia and its close allies to test the monophyly of the currently recognized genera,especially Photinia and Stranvaesia,and the hybrid origin hypothesis of Photinia bodinieri.This study employs complete plastomes and the entire nuclear ribosomal DNA(nrDNA)repeats assembled from the genome skimming approach with a broad taxon sampling of 81 species in 30 genera of Rosaceae,especially Maleae.Based on three datasets,including the whole plastome,coding sequence,and nrDNA repeats,the results of maximum likelihood and Bayesian inference analyses showed that the previously circumscribed Stranvaesia and Photinia were each non-monophyletic.Six clades have been recovered herein within Photinia and its allied genera:Aronia,Heteromeles,Photinia s.s.,Pourthiaea,Stranvaesia,and a new genus Phippsiomeles consisting of the Central American species formerly placed in Photinia.The strong conflicts between the plastome and nrDNA phylogenies of Phippsiomeles and Stranvaesia tomentosa suggest the possibility that they may have each originated involving hybridization events,while no incongruence among datasets was detected to support the hybrid origin of Photinia bodinieri.We provide 12 new combinations,to transfer eight taxa of the New World Photinia into Phippsiomeles and clarify the generic placements of several species of Photinia and Stranvaesia. | Bin-Bin Liu De-Yuan Hong Shi-Liang Zhou Chao Xu Wen-Pan Dong Gabriel Johnson and Jun Wen | 2019 | Journal of Systematics and Evolution2019，57，6： | 6 |
| 3 | Phylogeny and spatio-temporal diversification of Prunus subgenus Laurocerasus section Mesopygeum (Rosaceae) in the Malesian region显示文摘The goals of this study were to reconstruct the phylogeny of Prunus subgenus Laurocerasus section Mesopygeum and to provide a preliminary assessment of its spatio-temporal diversification in the Malesian region.We inferred the phylogeny using nuclear ITS and ETS and plastid psbA-trnH,rps16,rph6,and trnC-petN sequences.Our analyses support the monophyly of sect.Mesopygeum.Within sect.Mesopygeum,we identified four main subclades: (i)Prunus lancilimba from continental Asia;(ii)Prunus ruthii from Malay Peninsula;(iii)a subclade comprising species from areas centered on the Sunda shelf and also a few species from continental Asia and Wallacea;and (iv)a subclade composed of species from areas of the Sahul shelf,with a small number of taxa also from areas of the Sunda shelf, continental Asia,and the Philippines.We estimated that sect.Mesopygeum originated in continental Asia at c.44.71 Mya (95%HPD-31.66-46.90).Nine dispersals between maior geographic areas were inferred.From continental Asia, three and two dispersals were inferred to the 5unda shelf and the Sahul shelf in the mid-Oligocene,respectively.Two dispersals were inferred from the Sahul shelf region to the Sunda shelf in late Oligecene and early Miocene, respectively.There were also two dispersals inferred from the Sunda shelf region,one to the Philippines and one to Wallacea,in the middle and late Miocene,respectively.The diversification in sect.Mesopygeum was likely driven by active geologic events and orogenies in the Neogene in the Malesian region. | Liang Zhao Daniel Potter Yuan Xu Pei-Liang Liu Gabriel Johnson Zhao-Yang Chang Jun Wen | 2018 | Journal of Systematics and Evolution2018，56，6： | 5 |
| 4 | Molecular basis of chemosensitivity of platimum pre-treated ovarian cancer to chemotherapy 显示文摘 | Glaysher S Gabriel FG Johnson P | 2010 | Br J Cancer2010，103，5： | 1 |
| 5 | 3D- mapping optimization of embodied energy of transportation 显示文摘 | Joshua M Pearce Sara Johnson Gabriel B Grant | 2007 | Resources Conservation and Recycling2007，51，2： | 1 |
| 6 | Microscopic enteritis:Bucharest consensus显示文摘Microscopic enteritis(ME) is an inflammatory condition of the small bowel that leads to gastrointestinal symptoms,nutrient and micronutrient deficiency.It is characterised by microscopic or sub-microscopic abnormalities such as microvillus changes and enterocytic alterations in the absence of definite macroscopic changes using standard modern endoscopy.This work recognises a need to characterize disorders with microscopic and submicroscopic features,currently regarded as functional or non-specific entities,to obtain further understanding of their clinical relevance.The consensus working party reviewed statements about the aetiology,diagnosis and symptoms associated with ME and proposes an algorithm for its investigation and treatment.Following the 5th International Course in Digestive Pathology in Bucharest in November 2012,an international group of 21 interested pathologists and gastroenterologists formed a working party with a view to formulating a consensus statement on ME.A five-step agreement scale(from strong agreement to strong disagreement) was used to score 21 statements,independently.There was strong agreement on all statements about ME histology(95%-100%).Statements concerning diagnosis achieved 85% to 100% agreement.A statement on the management of ME elicited agreement from the lowest rate(60%) up to 100%.The remaining two categories showed general agreement between experts on clinical presentation(75%-95%) and pathogenesis(80%-90%) of ME.There was strong agreement on the histological definition of ME.Weaker agreement on management indicates a need for further investigations,better definitions and clinical trials to produce quality guidelines for management.This ME consensus is a step toward greater recognition of a significant entity affecting symptomatic patients previously labelled as non-specific or functional enteropathy. | Kamran Rostami David Aldulaimi Geoffrey Holmes Matt W Johnson Marie Robert Amitabh Srivastava Jean-Francois Fléjou David S Sanders Umberto Volta Mohammad H Derakhshan James J Going Gabriel Becheanu Carlo Catassi Mihai Danciu Luke Materacki Kamran Ghafarzadegan Sauid Ishaq Mohammad Rostami-Nejad A Salvador Pe?a Gabrio Bassotti Michael N Marsh Vincenzo Villanacci | 2015 | World Journal of Gastroenterology2015，21，9： | 1 |
| 7 | HIF1α Induces the Recruitment of Bone Marrow-Derived Vascular Modulatory Cells to Regulate Tumor Angiogenesis and Invasion显示文摘 | Rose Du Kan V. Lu Claudia Petritsch Patty Liu Ruth Ganss Emmanuelle Passegué Hanqiu Song Scott VandenBerg Randall S. Johnson Zena Werb Gabriele Bergers | 2008 | Cancer Cell2008，，3： | 1 |
| 8 | Effect of ramipril vs amlodipine on renal outcomes in hypertensive nephrosclerosis :A randomized controlled trial显示文摘 | Agodoa LY Appel L Bakris GL Beck G Bourgoignie J Briggs JP Charleston J Cheek D Cleveland W Douglas JG Douglas M Dowie D Faulkner M Gabriel A Gassman J Greene T Hall Y Hebert L Hiremath L Jamerson K Johnson CJ Kopple J Kusek J Lash J Lea J Lewis JB Lipkowitz M Massry S Middleton J Miller ER 3rd Norris K O'Connor D Ojo A Phillips RA Pogue V Rahman M Randall OS Rostand S Schulman G Smith W Thornley-Brown D Tisher CC Toto RD Wright JT Jr Xu S African American Study of Kidney Disease and Hypertension (AASK) Study Group | 2001 | JAMA2001，285，21： | 1 |
| 9 | Molecular basis of chemosensitivity of platinum pre-treated ovarian cancer to chemotherapy显示文摘 | Glaysher S Gabriel FG Johnson P | 2010 | Br J Cancer2010，103，5： | 1 |
| 10 | Management of invasive candidiasis and candidemia in adult non-neutropenic intensive care unit patients: Part I. Epidemiology and diagnosis显示文摘 | Beno?t P. Guery Maiken C. Arendrup Georg Auzinger élie Azoulay Márcio Borges Sá Elizabeth M. Johnson Eckhard Müller Christian Putensen Coleman Rotstein Gabriele Sganga Mario Venditti Rafael Zaragoza Crespo Bart Jan Kullberg | 2009 | Intensive Care Medicine2009，，1： | 1 |
| 11 | Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone显示文摘The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene,but early diversifications of the temperate biome under global climate change and biome shift remain uncertain.Moreover,it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity.Here,we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis,a charismatic component of the temperate North American flora with known and suspected gene flow among species.Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene,followed by widespread extinction and survival of relicts in the tropical New World.During the climate warming in the early Miocene,a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region.We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis.Furthermore,the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes.Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis,which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere.The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene. | Ze-Long Nie Richard Hodel Zhi-Yao Ma Gabriel Johnson Chen Ren Ying Meng Stefanie M.Ickert-Bond Xiu-Qun Liu Elizabeth Zimmer Jun Wen | 2023 | Journal of Integrative Plant Biology2023，65，5： | 1 |
| 12 | The fleet assignment problem: Solving a large-scale integer program显示文摘 | Christopher A. Hane Cynthia Barnhart Ellis L. Johnson Roy E. Marsten George L. Nemhauser Gabriele Sigismondi | 1995 | Mathematical Programming (-)1995，，1： | 1 |
| 13 | Dispersal and adaptive radiation of Bidens(Compositae)across the remote archipelagoes of Polynesia显示文摘The genus Bidens(Compositae)comprises c.230 species distributed across five continents,with the 41 Polynesian species displaying the greatest ecomorphological variation in the group.However,the genus has had a long and complicated taxonomic history,and its phylogenetic and biogeographic history are poorly understood.To resolve the evolutionary history of the Polynesian Bidens,152 individuals representing 91 species were included in this study,including 39 of the 41 described species from Polynesia.Four chloroplast and two nuclear DNA markers were utilized to estimate phylogenetic relationships,divergence times,and biogeographic history.Bidens was found to be polyphyletic within Coreopsis,consistent with previous assessments.The Polynesian radiation was resolved as monophyletic,with the initial dispersal into the Pacific possibly from South America to either the Hawaiian or Marquesas Islands.From the Marquesas,Bidens dispersed to the Society Islands,and ultimately to the Austral Islands.The initial diversification of the crown group in the Pacific is estimated to have occurred^1.63 mya(0.74-2.72,95%HPD),making Polynesian Bidens among the youngest and most rapid plant diversification events documented in the Pacific.Our findings suggest that relatively rare long-distance dispersal and founder-event speciation,coupled with subsequent loss of dispersal potential and within-island speciation,can explain the repeated and explosive adaptive radiation of Bidens throughout the archipelagoes of Polynesia. | Matthew L.Knope Vicki A.Funk Melissa A.Johnson Warren L.Wagner Erin M.Datlof Gabriel Johnson Daniel J.Crawford JMauricio Bonifacino Clifford W.Morden David H.Lorence Kenneth R.Wood Jean-Yves Meyer Sherwin Carlquist | 2020 | Journal of Systematics and Evolution2020，58，6： | 0 |
| 14 | Phylogenomics of Perityleae(Compositae)provides new insights into morphological and chromosomal evolution of the rock daisies显示文摘Rock daisies(Perityleae;Compositae)are a diverse clade of seven genera and ca.84 minimum-rank taxa that mostly occur as narrow endemics on sheer rock cliffs throughout the southwest United States and northern Mexico.Taxonomy of Perityleae has traditionally been based on morphology and cytogenetics.To test taxonomic hypotheses and utility of characters emphasized in past treatments,we present the first densely sampled molecular phylogenies of Perityleae and reconstruct trait and chromosome evolution.We inferred phylogenetic trees from whole chloroplast genomes,nuclear ribosomal cistrons,and hundreds of low-copy nuclear genes using genome skimming and target capture.Discordance between sources of molecular data suggests an underappreciated history of hybridization in Perityleae.Phylogenies support the monophyly of subtribe Peritylinae,a distinctive group possessing a four-lobed disc corolla;however,all of the phylogenetic trees generated in this study reject the monophyly of the most species-rich genus,Perityle,as well as its sections:Perityle sect.Perityle,Perityle sect.Laphamia,and Perityle sect.Pappothrix.Using reversible jump MCMC,our results suggest that morphological characters traditionally used to classify members of Perityleae have evolved multiple times within the group.A base chromosome number x=9 gave rise to higher base numbers in subtribe Peritylinae(x=12,13,16,17,18,and 19)through polyploidization,followed by ascending or descending dysploidy.Most taxa constitute a monophyletic lineage with a base chromosome number of x=17,with multiple neo-polyploidization events.These results demonstrate the advantages and obstacles of next-generation sequencing approaches in synantherology while laying the foundation for taxonomic revision and comparative study of the evolutionary ecology of Perityleae. | Isaac H.Lichter-Marck William A.Freyman Carolina M.Siniscalchi Jennifer R.Mandel Arturo Castro-Castro Gabriel Johnson Bruce G.Baldwin | 2020 | Journal of Systematics and Evolution2020，58，6： | 0 |
| 15 | Analysis of Soil Water Dynamics in a Tropical Rain Forest Soil (Arinic lixisol), Abeokuta, Nigeria显示文摘 | Sobowale Adeyinka Adewumi Johnson Kayode Ogunniranye Gabriel Bayo Sajo Opeyemi Samuel | 2014 | Journal of Agricultural Science and Technology(A)2014，4，6： | 0 |
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