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Systematics of the avian family Alaudidae using multilocus and genomic data

Avian Research 2023年第2期14卷 137-152页

作者： per alstrom.zeinolabedin m.ham.adi Erik D.Enbody martin Irestedt Derek Engelbrecht Pierre-Andre Crochet Alban Guillaumet Loïs Rancilhac B.Irene Tieleman Urban Olsson Paul F.Donald martin Stervander Animal Ecology Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityNorbyvagen 18DSE-75236UppsalaSweden Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing100101China Department of Biology Faculty of SciencesGolestan UniversityGorganGolestanIran Department of medical Biochemistry and microbiology Uppsala University75123UppsalaSweden Department of Biomolecular Engineering University of CaliforniaSanta Cruz95060Santa CruzCAUSA Department of Bioinformatics and Genetics Swedish Museum of Natural HistoryP.O.Box 50007SE-10405StockholmSweden Department of Biodiversity University of LimpopoPrivate Bag X1106Sovenga0727South Africa CEFE CNRSUniv MontpellierEPHEIRDMontpellierFrance Department of Biological&Environmental Sciences Troy UniversityTroyAL36082USA Groningen Institute for Evolutionary Life Sciences University of GroningenNijenborgh 79747 AGGroningenthe Netherlands Department of Biological and Environmental Sciences University of GothenburgP.O.Box 463SE-40530GothenburgSweden Gothenburg Global Biodiversity Centre P.O.Box 461SE-40530GothenburgSweden BirdLife International The David Attenborough BuildingPembroke StCambridgeCB23QZUK Department of Zoology University of CambridgeDowning StreetCambridgeCB23EJUK Bird Group Natural History MuseumAkeman StreetTringHertfordshireHP236APUnited Kingdom

The family Alaudidae,larks,comprises 93-100 species(depending on taxonomy)that are widely distributed across Africa and Eurasia,with single species extending their ranges to North and northernmost South America and Australia.A decade-old molecular phylogeny,comprising~80%of the species,revealed multiple cases of parallel evolution and large variation in rates of morphological evolution,which had misled taxonomists into creating many non-monophyletic ***,we reconstruct the phylogeny of the larks,using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species(in total 133 taxa;not all loci available for all species).We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling(in total 51 samples of 44 taxa across 40 species).Our results confirm the previous findings of rampant morphological convergence and divergence,and reveal new cases of paraphyletic *** propose a new subfamily classification,and also that the genus mirafra is divided into four genera to produce a more balanced generic classification of the *** study supports recently proposed species splits as well as some recent lumps,while also questioning some of the *** comprehensive phylogeny will form an important basis for future studies,such as comparative studies of lark natural history,ecology,evolution and conservation.

关键词： Phylogeny Phylogenomics multispecies coalescent Lark Paraphyly Taxonomy Subfamily description

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Elevational patterns of bird species richness on the eastern slope of ***,Sichuan Province,China

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Avian Research 2019年第1期10卷 1-12页

作者： Xingcheng He Xiaoyi Wang Shane DuBay Andrew Hart Reeve per alstrom Jianghong Ran Qiao Liu Yongjie Wu Key Laboratory of Bio-resources and Eco-environment of ministry of Education College of Life SciencesSichuan University Committee on Evolutionary Biology University of Chicago Life Sciences Section Integrative Research CenterField Museum of Natural History Biosystematics Section Natural History Museum of DenmarkUniversity of Copenhagen Department of Ecology and Genetics Animal EcologyEvolutionary Biology CentreUppsala University Swedish Species Information Centre Swedish University of Agricultural Sciences Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of Sciences Institute of mountain Hazards and Environment Chinese Academy of Sciences

Background:In biological systems,biological diversity often displays a rapid turn-over across *** defining feature has made mountains classic systems for studying the spatial variation in *** patterns of elevational diversity can vary among lineages and mountain systems it remains difficult to extrapolate findings from one montane region to another,or among *** this study,we assessed patterns and drivers of avian diversity along an elevational gradient on the eastern slope of ***,the highest peak in the Hengduan mountain Range in central China,and a mountain where comprehensive studies of avian diversity are still ***:We surveyed bird species in eight 400-m elevational bands from 1200 to 4400 m *** 2012 and *** test the relationship between bird species richness and environmental factors,we examined the relative importance of seven ecological variables on breeding season distribution patterns:land area(LA),mean daily temperature(mDT),seasonal temperature range(STR),the mid-domain effect(mDE),seasonal precipitation(SP),invertebrate biomass(IB) and enhanced vegetation index(EVI).Climate data were obtained from five local meteorological stations and three temperature/relative humidity smart sensors in ***:A total of 219 bird species were recorded in the field,of which 204 were recorded during the breeding season(April–August).Species richness curves(calculated separately for total species,large-ranged species,and smallranged species) were all ***-ranged species contributed more to the total species richness pattern than small-ranged *** and IB were positively correlated with total species richness and small-ranged species *** and mDT were positively correlated with small-ranged species richness,while STR and SP were negatively correlated with small-ranged species *** was positively correlated with large-ranged species *** we considered the combina

关键词： mt.Gongga Elevational gradient Environmental factors Species richness Stable microclimate

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Integrative taxonomy of the Plain-backed Thrush(Zoothera mollissima)complex(Aves,Turdidae)reveals cryptic species,including a new species

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Chinese Birds 2016年第1期7卷 2-39,1页

作者： per alstrom Pamela C.Rasmussen Chao Zhao Jingzi Xu Shashank Dalvi Tianlong Cai Yuyan Guan Ruiying Zhang mikhail V.Kalyakin Fumin Lei Urban Olsson Department of Animal Ecology Evolutionary Biology CentreUppsala University Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of Sciences Swedish Species Information Centre Swedish University of Agricultural Sciences Department of Integrative Biology and mSU museum Michigan State University Bird Group The Natural History Museum at Tring Cloud mountain Conservation Department of Evolutionary Biology Evolutionary Biology CentreUppsala University Researchers for Wildlife Conservation F-21National Centre for Biological Sciences College of Life Sciences University of Chinese Academy of Sciences Zoological museum of Lomonosov moscow State University Systematics and Biodiversity Department of Biology and Environmental SciencesUniversity of Gothenburg

Background: The Plain-backed Thrush Zoothera mollissima breeds in the Himalayas and mountains of central China. It was long considered conspecific with the Long-tailed Thrush Zoothera dixoni, until these were shown to be broadly ***: We revise the Z. mollissima–Z. dixoni complex by integrating morphological, acoustic, genetic(two mitochondrial and two nuclear markers), ecological and distributional ***: In earlier field observations, we noted two very different song types of "Plain-backed" Thrush segregated by breeding habitat and elevation. Further integrative analyses congruently identify three groups: an alpine breeder in the Himalayas and Sichuan, China("Alpine Thrush"); a forest breeder in the eastern Himalayas and northwest Yunnan(at least), China("Himalayan Forest Thrush"); and a forest breeder in central Sichuan("Sichuan Forest Thrush"). Alpine and Himalayan Forest Thrushes are broadly sympatric, but segregated by habitat and altitude, and the same is probably true also for Alpine and Sichuan Forest Thrushes. These three groups differ markedly in morphology and songs. In addition, DNA sequence data from three non-breeding specimens from Yunnan indicate that yet another lineage exists("Yunnan Thrush"). However, we find no consistent morphological differences from Alpine Thrush, and its breeding range is unknown. molecular phylogenetic analyses suggest that all four groups diverged at least a few million years ago, and identify Alpine Thrush and the putative "Yunnan Thrush" as sisters, and the two forest taxa as sisters. Cytochrome b divergences among the four Z. mollissima sensu lato(s.l.) clades are similar to those between any of them and Z. dixoni, and exceed that between the two congeneric outgroup species. We lectotypify the name Oreocincla rostrata Hodgson, 1845 with the Z. mollissima sensu stricto(s.s.) specimen long considered its type. No available name unambiguously pertains to the Himalayan Forest ***: The

关键词： Systematics morphology Bioacoustics Altitudinal distributions Genetic distances Undescribed taxa Zoothera dixoni Lectotypification Holotype

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This year's Nobel Prize to gastroenterology:Robin Warren and Barry marshall awarded for their discovery of Helicobacter pylori as pathogen in the gastrointestinal tract

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World Journal of Gastroenterology 2006年第19期12卷 3126-3127页

作者： per m Hellstr(o|¨)m Department of medicine Unit of Gastroenterology and Hepatology Karolinska University HospitalSolnaStockholmSweden

TO THE EDITORPeptic ulcer disease is a major health care concern in the society today, in view of personal suffering as well as economical health care costs.

关键词： Helicobacter pylori Nobel Prize Gastroenterology Helicobacter Infections History, 21st Century Humans Inflammation Peptic Ulcer Stomach Neoplasms

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BOUNDARY PROCEDURES FOR THE TImE-DEPENDENT BURGERS' EQUATION UNDER UNCERTAINTY

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Acta mathematica Scientia 2010年第2期30卷 539-550页

作者： per Pettersson Jan Nordstrm Gianluca Iaccarino mechanical Engineering and Institute for Computational mathematical Engineering Stanford University Division of Scientific Computing Department of Information TechnologyUppsala University School of mechanical Industrial and Aeronautical EngineeringUniversity of the Witvatersrand Department of Aeronautics and Systems Integration FOIThe Swedish Defense Research Agency

The Burgers＇ equation with uncertain initial and boundary conditions is approximated using a Polynomial Chaos Expansion （PCE） approach where the solution is represented as a series of stochastic, orthogonal polynomials. The resulting truncated PCE system is solved using a novel numerical discretization method based on spatial derivative operators satisfying the summation by parts property and weak boundary conditions to ensure stability. The resulting PCE solution yields an accurate quantitative description of the stochastic evolution of the system, provided that appropriate boundary conditions are available. The specification of the boundary data is shown to influence the solution; we will discuss the problematic implications of the lack of precisely characterized boundary data and possible ways of imposing stable and accurate boundary conditions.

关键词： stochastic Burgers' equation uncertainty quantification polynomial chaos

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Laparoscopic distal pancreatectomy for adenocarcinoma of the pancreas

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World Journal of Gastroenterology 2014年第37期20卷 13402-13411页

作者： Bergthor Bjrnsson per Sandstrm Department of Surgery County Council of stergtland and Department of Clinical and Experimental MedicineFaculty of Health SciencesLinkping University

Since the first report on laparoscopic distal pancreatectomy (LDP) appeared in the 1990s, the procedure has been performed increasingly frequently to treat both benign and malignant lesions of the pancreas. many earlier publications have shown LDP to be a good alternative to open distal pancreatectomy for benign lesions, although this has never been studied in a prospective, randomized manner. The evidence for the use of LDP to treat adenocarcinoma of the pancreas is not as well established. The purpose of this review is to evaluate the current evidence for LDP in cases of pancreatic adenocarcinoma. We conducted a review of English language publications reporting LDP results between 1990 and 2013. All studies reporting results in patients with histologically proven pancreatic adenocarcinoma were included. Thirty-nine publications were found and included in the results for a total of 309 cases of pancreatic adenocarcinoma (potential double publications were not eliminated). most LDP procedures are performed in selected cases and generally involve smaller tumors than open distal pancreatectomy (ODP) procedures. Some of the papers report unselected cases and include procedures on larger tumors. The number of lymph nodes harvested using LDP is comparable to the number obtained with ODP, as is the frequency of R0 resections. Current data suggest that similar short term oncological results can be obtained using LDP as those obtained using ODP.

关键词： Adenocarcinoma of the pancreas Laparoscopy Distal pancreatectomy Surgical margins Pancreatic resection

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Taxonomy of the White-browed Shortwing(Brachypteryx montana)complex on mainland Asia and Taiwan:an integrative approach supports recognition of three instead of one species

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Avian Research 2018年第4期9卷 281-293页

作者： per alstrom Pamela C.Rasmussen Canwei Xia magnus Gelang Yang Liu Guoling Chen min Zhao Yan Hao Chao Zhao Jian Zhao Chengte Yao James A.Eaton Robert Hutchinson Fumin Lei Urban Olsson Department of Ecology and Genetics Animal EcologyEvolutionary Biology CentreUppsala UniversityNorbyvaen 18D752 36 UppsalaSweden Swedish Species Information Centre Swedish University of Agricultural Sciences(SLU)Box 7007750 07 UppsalaSweden Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijing 100101China Department of Integrative Biology and mSU museum Michigan State UniversityEast LansingMI 48864USA Bird Group The Natural History Museum at TringAkeman StreetTring HP23 6APUK ministry of Education Key Laboratory for Biodiversity and Ecological Engineering College of Life SciencesBeijing Normal UniversityBeijing 100875China Gothenburg Natural History museum Box 7283402 35 GoteborgSweden State Key Laboratory of Biocontrol Department of EcologySchool of Life SciencesSun Yat-sen UniversityGuangzhou 510275China University of Chinese Academy of Sciences Beijing 100049China Cloud mountain Conservation Dali 671003YunnanChina High-Altitude Experimental Station Endemic Species Research InstituteCOAChi-chi 55244TaiwanChina Birdtour Asia 17 Keats AvenueLittleoverDerby DE23 4EEUK Department of Biology and Environmental Sciences Systematics and BiodiversityUniversity of GothenburgBox 463405 30 GoeborgSweden

Background: The White-browed Shortwing(Brachypteryx montana) is widespread from the central Himalayas to the southeast Chinese mainland and the island of Taiwan, the Philippines and Indonesia. multiple subspecies are recognised, and several of these have recently been suggested to be treated as separate species based on differences in morphology and ***: We here analyse plumage, morphometrics, songs, two mitochondrial and two nuclear markers, and geographical distributions of the two mainland Asian taxa B. m. cruralis and B. m. sinensis and the Taiwan Residents B. m. ***: We conclude that these differ congruently in morphology, songs and DNA. male B. m. goodfellowi is the most divergent in plumage(sexually monomorphic, unlike the two others; male similar to female), and B. m. cruralis and B. m. sinensis differ in male plumage maturation. The song of B. m. cruralis is strongly divergent from the others, whereas the songs of B. m. sinensis and B. m. goodfellowi are more similar to each other. Brachypteryx m. sinensis and B. m. goodfellowi are sisters, with an estimated divergence time 4.1 million years ago(mya; 95% highest posterior distribution [HPD] 2.8–5.5 mya), and B. m. cruralis separated from these two 5.8 mya(95% HPD 4.1–7.5 mya). We also report notable range extensions of B. m. sinensis as well as sympatry between this taxon and B. m. cruralis in Sichuan Province, China. Brachypteryx m. montana from Java is found to be more closely related to Lesser Shortwing(B. leucophris) and Rusty-bellied Shortwing(B. hyperythra) than to the mainland Asian and Taiwan Residents ***: Our data support a recent proposal to treat the three mainland Asian and Taiwan Residents taxa as three species, separate from B. montana sensu stricto: B. cruralis(central Himalayas to south central China and south Vietnam), B. sinensis(north central to southeastern part of China's mainland) and B. goodfellowi(Taiwan Island).

关键词： Integrative taxonomy morphology Song miocene Pliocene

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Dysregulation of gastric H,K-ATPase by cigarette smoke extract

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World Journal of Gastroenterology 2009年第32期15卷 4016-4022页

作者： muna hammadi mohamed adi Rony John Ghalia AK Khoder Sherif m Karam Department of Anatomy Faculty of Medicine & Health SciencesUAE UniversityAl-AinPO Box 17666United Arab Emirates

AIm:To test whether the expression and activity of H,K-ATPase in parietal cells would be affected by cigarette smoke ***: Extracts of cigarette smoke were administered into mice by gastric gavage (5 mg/kg body weight/day) for 3 d or in drinking water for 7 or 14 d. For the latter, each day a mouse consumed 5 mL water containing extracts of two cigarettes, on average. Control littermate mice received only vehicle. To compare the amount of H,K-ATPase in control and smoke-treated mice, the stomach was processed for Western blotting and immunohistochemical analysis using monoclonal antibodies specific for α- or β-subunits of H,K-ATPase. The p-nitrophenylphospatase activity assay was used as a measurement for K-dependent H,K-ATPase ***: Probed transblots showed an increase in the amount of H,K-ATPase in smoke-treated mice which was confirmed by immunohistochemistry and was found to be due to increased amounts of protein per parietal cell rather than an increased parietal cell number. The increase in the amount of H,K-ATPase was associated with an enhancement of its enzymatic activity. K-dependent activity in control and smoke-treated mice was significantly different (respectively, 0.12 μmol/mg vs 0.27 μmol/mg per minute, Pministration of cigarette smoke extract is associated with an increase in the amount and activity of H,K-ATPase and hence, smokers are susceptible to development of peptic ulcer.

关键词： Proton pump H,K-ATPase Parietal cell Gastric gland Oxyntic mucosa Cigarette smoke extract Smoking

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A direct solver with O（N） complexity for integral equations on one-dimensional domains

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Frontiers of mathematics in China 2012年第2期7卷 217-247页

作者： Adrianna GILLmAN Patrick m. YOUNG per-Gunnar mARTINSSON Department of Applied mathematics University of Colorado at Boulder BoulderCO 80309-0526 USA

An algorithm for the direct inversion of the linear systems arising from NystrSm discretization of integral equations on one-dimensional domains is described. The method typically has O（N） complexity when applied to boundary integral equations （BIEs） in the plane with non-oscillatory kernels such as those associated with the Laplace and Stokes＇ equations. The scaling coefficient suppressed by the ＂big-O＂ notation depends logarithraically on the requested accuracy. The method can also be applied to BIEs with oscillatory kernels such as those associated with the Helmholtz and time-harmonic maxwell equations; it is efficient at long and intermediate wave-lengths, but will eventually become prohibitively slow as the wave-length decreases. To achieve linear complexity, rank： deficiencies in the off-diagonal blocks of the coefficient matrix are exploited. The technique is conceptually related to the H- and H2-matrix arithmetic of Hackbusch and coworkers, and is closely related to previous work on Hierarchically Semi-Separable matrices.

关键词： Direct solver integral equation fast direct solver boundary value problem boundary integral equation hierarchically semi-separable matrix mSC 65R20,65F05

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Integrative taxonomy of the Russet Bush Warbler Locustella mandelli complex reveals a new species from central China

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Chinese Birds 2015年第2期6卷 60-91页

作者： per alstrom Canwei Xia Pamela C Rasmussen Urban Olsson Bo Dai Jian Zhao Paul J Leader Geoff J Carey Lu Dong Tianlong Cai Paul I Holt Hung Le manh Gang Song Yang Liu Yanyun Zhang Fumin Lei Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of Sciences Swedish Species Information Centre Swedish University of Agricultural Sciences ministry of Education Key Laboratory for Biodiversity and Ecological Engineering College of Life SciencesBeijing Normal University Department of Integrative Biology and mSU museum Michigan State University Bird Group The Natural History Museum at Tring Department of Biology and Environmental Sciences Systematics and BiodiversityUniversity of Gothenburg College of Life Sciences Leshan Normal University State Key Laboratory of Biocontrol and College of Ecology and Evolution Sun Yat-sen University c/o AEC Ltd 121–127 Commercial CentrePalm SpringsYuen LongHong Kong College of Life Sciences University of Chinese Academy of Sciences Bracken Dean PendletonClitheroeLancashire BB7 1PTUK Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology

Background: The Russet Bush Warbler Locustella(previously Bradypterus) mandelli complex occurs in mountains in the eastern Himalayas, southern China, Vietnam, the Philippines, and Indonesia. The taxonomy has been debated,with one(L. seebohmi) to four(L. seebohmi, L. mandelli, L. montis and L. timorensis) species having been ***: We used an integrative approach, incorporating analyses of morphology, vocalizations and a molecular marker, to re-evaluate species limits in the L. mandelli ***: We found that central Chinese L. mandelli differed from those from India through northern Southeast Asia to southeast China in plumage, morphometrics and song. All were easily classified by song, and(wing + culmen)/tail ratio overlapped only marginally. Both groups were reciprocally monophyletic in a mitochondrial cytochrome b(cytb) gene tree, with a mean divergence of 1.0 ± 0.2%. They were sympatric and mostly altitudinally segregated in the breeding season in southern Sichuan province. We found that the mt Victoria(western myanmar) population differed vocally from other L. mandelli, but no specimens are available. Taiwan Bush Warbler L. alishanensis was sister to the L. mandelli complex, with the most divergent song. Plumage, vocal and cytb evidence supported the distinctness of the south Vietnamese L. mandelli idonea. The Timor Bush Warbler L. timorensis, Javan Bush Warbler *** and Benguet Bush Warbler L. seebohmi differed distinctly in plumage, but among-population song variation in L. montis exceeded the differences between some populations of these taxa, and mean pairwise cytb divergences were only 0.5–0.9%. We also found that some L. montis populations differed ***: We conclude that the central Chinese population of Russet Bush Warbler represents a new species,which we describe herein, breeding at mid elevations in Sichuan, Shaanxi, Hubei, Hunan and Guizhou *** taxonomic status of the other allopatric populati

关键词： Bradypterus Cryptic species Locustella seebohmi Locustella mandelli Locustella montis Locustella timorensis Locustella alishanen

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