[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"_public_publisher_byId_b9d49dfa-198f-4150-8000-dd7a5a70898c":3,"_public_publication_all{\"sortAscending\":false,\"sortField\":\"updateTime\",\"page\":0,\"size\":10,\"facet\":true,\"searchKey\":\"publisherId:b9d49dfa-198f-4150-8000-dd7a5a70898c,\"}":106},{"code":4,"data":5,"meta":18},"SUCCESS",{"id":6,"createTime":7,"updateTime":8,"relativeEntities":9,"slug":10,"properties":11,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":20,"manageAffiliations":21,"indexDatabases":22,"url":18,"thumbnailPath":18,"statistic":38,"gsStatistic":18,"type":18,"analyzePriority":18},"b9d49dfa-198f-4150-8000-dd7a5a70898c","2024-04-14T07:20:36.136+00:00","2025-11-21T09:52:28.691+00:00",[],"Springer-Science-and-Business-Media-LLC",{"title":12,"eissn":14},{"EN":13},"Springer Science and Business Media LLC",{"VOID":15},"1471-2148","PUBLISHER","PENDING",null,0,[],[],[23],{"id":24,"indexDatabase":25,"url":35,"indexYears":36,"academicFieldIds":18,"indexDatabaseRanking":37},"727c9e56-aaba-4364-888a-09bd3d185760",{"id":26,"createTime":18,"updateTime":18,"relativeEntities":27,"label":28,"description":30,"key":32,"publicationTags":33,"standard":18},"3c7051d4-eb7d-4c57-a56b-36fc74c5d1e9",[],{"EN":29,"VI":29},"Scopus - Elsevier",{"EN":29,"VI":31},"Cơ sở dữ liệu Scopus thuộc Elsevier","scopus",[34],"SCOPUS","https:\u002F\u002Fwww.scopus.com\u002Fsourceid\u002F21724","2001-2020","SCOPUS__Q1",{"impactFactor":19,"impactFactorByYear":39,"i10Index":51,"i10IndexLast5Year":52,"totalPublication":53,"totalPublicationByYear":54,"totalCitation":70,"totalCitationByYear":71,"totalCitationPerPublication":88,"totalCitationPerPublicationByYear":89,"hindexLast5Year":105,"hindex":105},{"2012":40,"2013":41,"2014":42,"2015":43,"2016":44,"2017":45,"2018":46,"2019":47,"2020":48,"2021":49,"2022":50},4.12,4.28,2.75,2.95,3.43,3.9,4.1,4.27,4.11,3.34,3,312,26,379,{"2005":55,"2006":56,"2007":57,"2008":58,"2009":59,"2010":60,"2011":61,"2012":62,"2013":63,"2014":64,"2015":65,"2016":66,"2017":67,"2018":68,"2019":69,"2020":62},7,4,11,31,14,18,42,23,13,25,43,30,38,24,33,14083,{"2005":72,"2006":73,"2007":74,"2008":75,"2009":76,"2010":77,"2011":78,"2012":79,"2013":80,"2014":81,"2015":82,"2016":83,"2017":84,"2018":85,"2019":86,"2020":87},283,752,1054,1636,959,832,1853,745,408,650,1351,983,1048,844,450,235,37.16,{"2005":90,"2006":91,"2007":92,"2008":93,"2009":94,"2010":95,"2011":96,"2012":97,"2013":98,"2014":52,"2015":99,"2016":100,"2017":101,"2018":102,"2019":103,"2020":104},40.43,188,95.82,52.77,68.5,46.22,44.12,32.39,31.38,31.42,32.77,27.58,35.17,13.64,10.22,60,{"meta":107,"data":109},{"total":108},"2905",[110,275,353,643,711,777,1189,1264,1420,1855],{"id":111,"createTime":112,"updateTime":113,"relativeEntities":114,"slug":115,"properties":116,"entityType":127,"verifyStatus":128,"verifyTime":129,"verifyNote":130,"languages":18,"translateLanguages":18,"viewCount":19,"primaryUrl":131,"fullTextUrl":18,"authors":132,"publicationType":241,"publisherRelationship":242,"citationCount":19,"citationInfo":267,"publishDate":270,"publishYear":268,"citationAnalyzeStatus":271,"lastCitationAnalyze":272,"indexDatabases":273,"openAccess":18,"references":18,"isForceReanalyzing":274},"628aa394-c21c-4d1c-808a-de8102d7c8f6","2024-02-07T17:45:21.851+00:00","2026-08-15T15:04:05.965+00:00",[],"Genome-wide-identification-and-evolution-of-ATP-binding-cassette-transporters-in-the-ciliate-Tetrahymena-thermophila-A-case-of-functional-divergence-in-a-multigene-family",{"abstract":117,"title":119,"gsPaper":121,"references":123,"doi":125},{"EN":118},"In eukaryotes, ABC transporters that utilize the energy of ATP hydrolysis to expel cellular substrates into the environment are responsible for most of the efflux from cells. Many members of the superfamily of ABC transporters have been linked with resistance to multiple drugs or toxins. Owing to their medical and toxicological importance, members of the ABC superfamily have been studied in several model organisms and warrant examination in newly sequenced genomes. A total of 165 ABC transporter genes, constituting a highly expanded superfamily relative to its size in other eukaryotes, were identified in the macronuclear genome of the ciliate Tetrahymena thermophila. Based on ortholog comparisons, phylogenetic topologies and intron characterizations, each highly expanded ABC transporter family of T. thermophila was classified into several distinct groups, and hypotheses about their evolutionary relationships are presented. A comprehensive microarray analysis revealed divergent expression patterns among the members of the ABC transporter superfamily during different states of physiology and development. Many of the relatively recently formed duplicate pairs within individual ABC transporter families exhibit significantly different expression patterns. Further analysis showed that multiple mechanisms have led to functional divergence that is responsible for the preservation of duplicated genes. Gene duplications have resulted in an extensive expansion of the superfamily of ABC transporters in the Tetrahymena genome, making it the largest example of its kind reported in any organism to date. Multiple independent duplications and subsequent divergence contributed to the formation of different families of ABC transporter genes. Many of the members within a gene family exhibit different expression patterns. The combination of gene duplication followed by both sequence divergence and acquisition of new patterns of expression likely plays a role in the adaptation of Tetrahymen a to its environment.",{"EN":120},"Genome-wide identification and evolution of ATP-binding cassette transporters in the ciliate Tetrahymena thermophila: A case of functional divergence in a multigene family",{"VOID":122},"[\"7511012577809754832\"]",{"VOID":124},"Holland IB, Blight MA: ABC-ATPases, adaptable energy generators fuelling transmembrane movement of a variety of molecules organisms from bacteria to humans. J Mol Biol. 1999, 293 (2): 381-399. 10.1006\u002Fjmbi.1999.2993.\nHollenstein K, Dawson RJP, Locher KP: Structure and mechanism of ABC transporter proteins. Curr Opin Struc Biol. 2007, 17 (4): 412-418. 10.1016\u002Fj.sbi.2007.07.003.\nKos V, Ford RC: The ATP-binding cassette family: a structural perspective. Cellular and Molecular Life Sciences. 2009, 66 (19): 3111-3126. 10.1007\u002Fs00018-009-0064-9.\nKlein I, Sarkadi B, Varadi A: An inventory of the human ABC proteins. Biochim Biophys Acta. 1999, 1461 (2): 237-262. 10.1016\u002FS0005-2736(99)00161-3.\nDean M, Hamon Y, Chimini G: The human ATP-binding cassette (ABC) transporter superfamily. Journal of Lipid Research. 2001, 42 (7): 1007-1017.\nGottesman MM, Ambudkar SV: Overview: ABC transporters and human disease. Journal of Bioenergetics and Biomembranes. 2001, 33 (6): 453-458. 10.1023\u002FA:1012866803188.\nGottesman MM, Fojo T, Bates SE: Multidrug resistance in cancer: Role of ATP-dependent transporters. Nature Reviews Cancer. 2002, 2 (1): 48-58. 10.1038\u002Fnrc706.\nJones PM, George AM: Multidrug resistance in parasites: ABC transporters, P-glycoproteins and molecular modelling. International Journal for Parasitology. 2005, 35 (5): 555-566. 10.1016\u002Fj.ijpara.2005.01.012.\nLanning CL, Fine RL, Corcoran JJ, Ayad HM, Rose RL, AbouDonia MB: Tobacco budworm P-glycoprotein: Biochemical characterization and its involvement in pesticide resistance. Biochimica Et Biophysica Acta-General Subjects. 1996, 1291 (2): 155-162. 10.1016\u002F0304-4165(96)00060-8.\nAurade R, Jayalakshmi SK, Sreeramulu K: Stimulatory effect of insecticides on partially purified P-glycoprotein ATPase from the resistant pest Helicoverpa armigera. Biochemistry and Cell Biology-Biochimie Et Biologie Cellulaire. 2006, 84 (6): 1045-1050. 10.1139\u002FO06-194.\nSreeramulu K, Srinivas R, Jayalakshmi SK: Effect of insecticides on P-glycoprotein ATPase activity of the insecticide resistant pest Helicoverpa armigera. Biochemistry and Cell Biology-Biochimie Et Biologie Cellulaire. 2006, 84 (6): 1059-1060.\nO'Connor R: The pharmacology of cancer resistance. Anticancer Research. 2007, 27 (3A): 1267-1272.\nFranke RM, Sparreboom A: Drug Transporters: Recent Advances and Therapeutic Applications. Clinical Pharmacology & Therapeutics. 2010, 87 (1): 3-7.\nKroetz D: Involvement of ABC transporters in pharmacokinetics and toxicokinetics. Toxicology Letters. 2009, 189: S17-S17. 10.1016\u002Fj.toxlet.2009.06.009.\nDean M, Annilo T: Evolution of the ATP-binding cassette (ABC) transporter superfamily in vertebrates. Annual Review of Genomics and Human Genetics. 2005, 6: 123-142. 10.1146\u002Fannurev.genom.6.080604.162122.\nRoth CW, Holm I, Graille M, Dehoux P, Rzhetsky A, Wincker P, Weissenbach J, Brey PT: Identification of the Anopheles gambiae ATP-binding cassette transporter superfamily genes. Molecules and Cells. 2003, 15 (2): 150-158.\nSheps JA, Ralph S, Zhao ZY, Baillie DL, Ling V: The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes. Genome Biology. 2004, 5 (3): R15-10.1186\u002Fgb-2004-5-3-r15.\nJungwirth H, Kuchler K: Yeast ABC transporters - A tale of sex, stress, drugs and aging. Febs Letters. 2006, 580 (4): 1131-1138. 10.1016\u002Fj.febslet.2005.12.050.\nMoussatova A, Kandt C, O'Mara ML, Tieleman DP: ATP-binding cassette transporters in Escherichia coli. Biochimica Et Biophysica Acta-Biomembranes. 2008, 1778 (9): 1757-1771. 10.1016\u002Fj.bbamem.2008.06.009.\nLinton KJ, Higgins CF: The Escherichia coli ATP-binding cassette (ABC) proteins. Molecular Microbiology. 1998, 28 (1): 5-13. 10.1046\u002Fj.1365-2958.1998.00764.x.\nDavidson AL, Chen J: ATP-binding cassette transporters in bacteria. Annual Review of Biochemistry. 2004, 73: 241-268. 10.1146\u002Fannurev.biochem.73.011303.073626.\nDavidson AL, Dassa E, Orelle C, Chen J: Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiology and Molecular Biology Reviews. 2008, 72 (2): 317-364. 10.1128\u002FMMBR.00031-07.\nPerez-Victoria JM, Parodi-Talice A, Torres C, Gamarro F, Castanys S: ABC transporters in the protozoan parasite Leishmania. Int Microbiol. 2001, 4 (3): 159-166.\nKlokouzas A, Shahi S, Hladky SB, Barrand MA, van Veen HW: ABC transporters and drug resistance in parasitic protozoa. International Journal of Antimicrobial Agents. 2003, 22 (3): 301-317. 10.1016\u002FS0924-8579(03)00210-3.\nCollins K, Gorovsky MA: Tetrahymena thermophila. Current Biology. 2005, 15 (9): R317-R318. 10.1016\u002Fj.cub.2005.04.039.\nFillingham JS, Chilcoat ND, Turkewitz AP, Orias E, Reith M, Pearlman RE: Analysis of expressed sequence tags (ESTs) in the ciliated protozoan Tetrahymena thermophila. Journal of Eukaryotic Microbiology. 2002, 49 (2): 99-107. 10.1111\u002Fj.1550-7408.2002.tb00350.x.\nEisen JA, Coyne RS, Wu M, Wu DY, Thiagarajan M, Wortman JR, Badger JH, Ren QH, Amedeo P, Jones KM, et al: Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. Plos Biology. 2006, 4 (9): 1620-1642. 10.1371\u002Fjournal.pbio.0040286.\nMiao W, Xiong J, Bowen J, Wang W, Liu Y, Braguinets O, Grigull J, Pearlman RE, Orias E, Gorovsky MA: Microarray analyses of gene expression during the Tetrahymena thermophila life cycle. PLoS ONE. 2009, 4 (2): e4429-10.1371\u002Fjournal.pone.0004429.\nStover NA, Krieger CJ, Binkley G, Dong Q, Fisk DG, Nash R, Sethuraman A, Weng S, Cherry JM: Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research. Nucleic Acids Research. 2006, D500-503. 10.1093\u002Fnar\u002Fgkj054. 34 Database\nFu CJ, Xiong J, Miao W: Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila. Bmc Genomics. 2009, 10: 208-10.1186\u002F1471-2164-10-208.\nSanchez-Fernandez R, Davies TGE, Coleman JOD, Rea PA: The Arabidopsis thaliana ABC protein superfamily, a complete inventory. Journal of Biological Chemistry. 2001, 276 (32): 30231-30244. 10.1074\u002Fjbc.M103104200.\nAnjard C, Loomis WF: Evolutionary analyses of ABC transporters of Dictyostelium discoideum. Eukaryotic Cell. 2002, 1 (4): 643-652. 10.1128\u002FEC.1.4.643-652.2002.\nGbelska Y, Krijger JJ, Breunig KD: Evolution of gene families: the multidrug resistance transporter genes in five related yeast species. Fems Yeast Research. 2006, 6 (3): 345-355. 10.1111\u002Fj.1567-1364.2006.00058.x.\nMengerink KJ, Vacquier VD: An ATP-binding cassette transporter is a major glycoprotein of sea urchin sperm membranes. Journal of Biological Chemistry. 2002, 277 (43): 40729-40734. 10.1074\u002Fjbc.M207184200.\nIwamoto M, Sugai T, Nakaoka Y: Cell division induced by mechanical stimulation in starved Tetrahymena thermophila: cell cycle without synthesis of macronuclear DNA. Cell Biology International. 2004, 28 (7): 503-509. 10.1016\u002Fj.cellbi.2004.04.004.\nCsere P, Lill R, Kispal G: Identification of a human mitochondrial ABC transporter, the functional orthologue of yeast Atm1p. FEBS Letters. 1998, 441 (2): 266-270. 10.1016\u002FS0014-5793(98)01560-9.\nMitsuhashi N, Miki T, Senbongi H, Yokoi N, Yano H, Miyazaki M, Nakajima N, Iwanaga T, Yokoyama Y, Shibata T, et al: MTABC3, a novel mitochondrial ATP-binding cassette protein involved in iron homeostasis. Journal of Biological Chemistry. 2000, 275 (23): 17536-17540. 10.1074\u002Fjbc.275.23.17536.\nPerez-Tomas R: Multidrug resistance: Retrospect and prospects in anti-cancer drug treatment. Current Medicinal Chemistry. 2006, 13 (16): 1859-1876. 10.2174\u002F092986706777585077.\nMcgrath JP, Varshavsky A: The Yeast Ste6 Gene Encodes a Homolog of the Mammalian Multidrug Resistance P-Glycoprotein. Nature. 1989, 340 (6232): 400-404. 10.1038\u002F340400a0.\nBamdad M, Reader S, Groliere CA, Bohatier J, Denizeau F: Uptake and efflux of polycyclic aromatic hydrocarbons by Tetrahymena pyriformis: Evidence for a resistance mechanism. Cytometry. 1997, 28 (2): 170-175. 10.1002\u002F(SICI)1097-0320(19970601)28:2\u003C170::AID-CYTO11>3.0.CO;2-N.\nBamdad M, Brousseau P, Denizeau F: Identification of a multidrug resistance-like system in Tetrahymena pyriformis: evidence for a new detoxication mechanism in freshwater ciliates. Febs Letters. 1999, 456 (3): 389-393. 10.1016\u002FS0014-5793(99)00978-3.\nLeslie EM, Deeley RG, Cole SPC: Multidrug resistance proteins: role of P-glycoprotein, MRP1, MRP2, and BCRP (ABCG2) in tissue defense. Toxicology and Applied Pharmacology. 2005, 204 (3): 216-237. 10.1016\u002Fj.taap.2004.10.012.\nDepeille P, Cuq P, Mary S, Passagne I, Evrard A, Cupissol D, Vian L: Glutathione S-transferase M1 and multidrug resistance protein 1 Act in synergy to protect melanoma cells from vincristine effects. Molecular Pharmacology. 2004, 65 (4): 897-905. 10.1124\u002Fmol.65.4.897.\nZolman BK, Silva ID, Bartel B: The Arabidopsis pxa1 mutant is defective in an ATP-binding cassette transporter-like protein required for peroxisomal fatty acid beta-oxidation. Plant Physiology. 2001, 127 (3): 1266-1278. 10.1104\u002Fpp.010550.\nHettema EH, Distel B, Tabak HF: Import of proteins into peroxisomes. Bba-Mol Cell Res. 1999, 1451 (1): 17-34.\nShani N, Valle D: A Saccharomyces cerevisiae homolog of the human adrenoleukodystrophy transporter is a heterodimer of two half ATP-binding cassette transporters. Proceedings of the National Academy of Sciences of the United States of America. 1996, 93 (21): 11901-11906. 10.1073\u002Fpnas.93.21.11901.\nDean M, Rzhetsky A, Allikmets R: The human ATP-binding cassette (ABC) transporter superfamily. Genome Res. 2001, 11 (7): 1156-1166. 10.1101\u002Fgr.GR-1649R.\nvan Roermund CWT, Visser WF, Ijlst L, van Cruchten A, Boek M, Kulik W, Waterham HR, Wanders RJA: The human peroxisomal ABC half transporter ALDP functions as a homodimer and accepts acyl-CoA esters. Faseb Journal. 2008, 22 (12): 4201-4208. 10.1096\u002Ffj.08-110866.\nBisbal C, Martinand C, Silhol M, Lebleu B, Salehzada T: Cloning and Characterization of a Rnase-L Inhibitor - a New Component of the Interferon-Regulated 2-5a Pathway. Journal of Biological Chemistry. 1995, 270 (22): 13308-13317. 10.1074\u002Fjbc.270.22.13308.\nMarton MJ, deAldana CRV, Qiu HF, Chakraburtty K, Hinnebusch AG: Evidence that GCN1 and GCN20, translational regulators of GCN4, function on elongating ribosomes in activation of eIF2 alpha kinase GCN2. Mol Cell Biol. 1997, 17 (8): 4474-4489.\nKage K, Tsukahara S, Sugiyama T, Asada S, Ishikawa E, Tsuruo T, Sugimoto Y: Dominant-negative inhibition of breast cancer resistance protein as drug efflux pump through the inhibition of S-S dependent homodimerization. International Journal of Cancer. 2002, 97 (5): 626-630. 10.1002\u002Fijc.10100.\nXu JK, Liu Y, Yang YY, Bates S, Zhang JT: Characterization of oligomeric human half-ABC transporter ATP-binding cassette G2. Journal of Biological Chemistry. 2004, 279 (19): 19781-19789. 10.1074\u002Fjbc.M310785200.\nQuentin Y, Fichant G: ABCdb: an ABC transporter database. J Mol Microb Biotech. 2000, 2 (4): 501-504.\nTomii K, Kanehisa M: A comparative analysis of ABC transporters in complete microbial genomes. Genome Res. 1998, 8 (10): 1048-1059.\nSaurin W, Hofnung M, Dassa E: Getting in or out: Early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters. J Mol Evol. 1999, 48 (1): 22-41. 10.1007\u002FPL00006442.\nVogel C, Bashton M, Kerrison ND, Chothia C, Teichmann SA: Structure, function and evolution of multidomain proteins. Curr Opin Struc Biol. 2004, 14 (2): 208-216. 10.1016\u002Fj.sbi.2004.03.011.\nGarcia O, Bouige P, Forestier C, Dassa E: Inventory and comparative analysis of rice Arabidopsis ATP-binding cassette (ABC) systems. J Mol Biol. 2004, 343 (1): 249-265. 10.1016\u002Fj.jmb.2004.07.093.\nBiemans-Oldehinkel E, Doeven MK, Poolman B: ABC transporter architecture and regulatory roles of accessory domains. FEBS Letters. 2006, 580 (4): 1023-1035. 10.1016\u002Fj.febslet.2005.11.079.\nSmith PC, Karpowich N, Millen L, Moody JE, Rosen J, Thomas PJ, Hunt JF: ATP binding to the motor domain from an ABC transporter drives formation of a nucleotide sandwich dimer. Mol Cell. 2002, 10 (1): 139-149. 10.1016\u002FS1097-2765(02)00576-2.\nNguyen HD, Yoshihama M, Kenmochi N: The evolution of spliceosomal Introns in alveolates. Molecular Biology and Evolution. 2007, 24 (5): 1093-1096. 10.1093\u002Fmolbev\u002Fmsm037.\nZufall RA, McGrath CL, Muse SV, Katz LA: Genome architecture drives protein evolution in ciliates. Molecular Biology and Evolution. 2006, 23 (9): 1681-1687. 10.1093\u002Fmolbev\u002Fmsl032.\nLynch M, Conery JS: The evolutionary fate and consequences of duplicate genes. Science. 2000, 290 (5494): 1151-1155. 10.1126\u002Fscience.290.5494.1151.\nMarques AC, Vinckenbosh N, Brawand D, Kaessmann H: Functional diversification of duplicate genes through subcellular adaptation of encoded proteins. Genome Biology. 2008, 9 (3): R54-10.1186\u002Fgb-2008-9-3-r54.\nInnan H, Kondrashov F: The evolution of gene duplications: classifying and distinguishing between models. Nature Reviews Genetics. 2010, 11 (2): 97-108.\nGu X: Statistical framework for phylogenomic analysis of gene family expression profiles. Genetics. 2004, 167 (1): 531-542. 10.1534\u002Fgenetics.167.1.531.\nOakley TH, Gu ZL, Abouheif E, Patel NH, Li WH: Comparative methods for the analysis of gene-expression evolution: An example using yeast functional genomic data. Molecular Biology and Evolution. 2005, 22 (1): 40-50. 10.1093\u002Fmolbev\u002Fmsh257.\nLynch M, Force A: The probability of duplicate gene preservation by subfunctionalization. Genetics. 2000, 154 (1): 459-473.\nHughes T, Liberles DA: The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo-than subfunctionalisation. J Mol Evol. 2007, 65 (5): 574-588. 10.1007\u002Fs00239-007-9041-9.\nKondrashov FA, Rogozin IB, Wolf YI, Koonin EV: Selection in the evolution of gene duplications. Genome Biology. 2002, 3 (2): RESEARCH0008-10.1186\u002Fgb-2002-3-2-research0008.\nVeitia RA: Gene dosage balance: deletions, duplications and dominance. Trends Genet. 2005, 21 (1): 33-35. 10.1016\u002Fj.tig.2004.11.002.\nConant GC, Wolfe KH: Functional partitioning of yeast co-expression networks after genome duplication. Plos Biology. 2006, 4 (4): 545-554. 10.1371\u002Fjournal.pbio.0040109.\nCapella-Gutierrez S, Silla-Martinez JM, Gabaldon T: trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009, 25 (15): 1972-1973. 10.1093\u002Fbioinformatics\u002Fbtp348.\nGuindon S, Dufayard JF, Hordijk W, Lefort V, Gascuel O: PhyML: Fast and Accurate Phylogeny Reconstruction by Maximum Likelihood. Infection Genetics and Evolution. 2009, 9 (3): 384-385.\nOrias E, Hamilton EP, Orias JD: Tetrahymena as a laboratory organism: Useful strains, cell culture, and cell line maintenance. Methods in Cell Biology, Vol 62. 2000, 62: 189-211. full_text.\nMiao W, Yu T, Orias E, Wan ML, Fu CJ: Identification of differentially expressed genes in Tetrahmena thermophila in response to dichlorodiphenyltrichloroethane (DDT) by suppression subtractive hybridization. Environmental Microbiology. 2006, 8 (6): 1122-1129. 10.1111\u002Fj.1462-2920.2006.00988.x.\nFeng LF, Miao W, Wu YX: Difterentially expressed genes of Tetrahymena thermophila in response to tributyltin (TBT) identified by suppression subtractive hybridization and real time quantitative PCR. Aquatic Toxicology. 2007, 81 (1): 99-105. 10.1016\u002Fj.aquatox.2006.11.005.\nPosada D, Crandall KA: MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998, 14 (9): 817-818. 10.1093\u002Fbioinformatics\u002F14.9.817.\nSwofford DL: PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta. 2001, Sinauer Associates, Sunderland, Mass\nLee C, Blay S, Mooers AO, Singh A, Oakley TH: CoMET: A Mesquite package for comparing models of continuous character evolution on phylogenies. Evol Bioinform Online. 2006, 2: 183-186.\nWP Maddison DM: Mesquite: a modular system for evolutionary analysis. Version 2.5. 2008, [http:\u002F\u002Fmesquiteproject.org]\nYang ZH: PAML: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences. 1997, 13 (5): 555-556.",{"VOID":126},"10.1186\u002F1471-2148-10-330","PUBLICATION","VERIFIED","2024-05-10T20:45:26.459+00:00","Auto Verify","https:\u002F\u002Fbmcecolevol.biomedcentral.com\u002Farticles\u002F10.1186\u002F1471-2148-10-330",[133,160,190,203,228],{"id":134,"sortIndex":19,"researcher":18,"roles":135,"affiliations":137,"properties":155},"bf7d274c-1a4b-4766-bf82-eb869733cbd6",[136],"AUTHOR",[138,146],{"id":139,"sortIndex":19,"affiliation":140,"properties":18},"289e27df-d181-445f-9f73-0e14f2b7c149",{"id":139,"createTime":18,"updateTime":18,"relativeEntities":141,"slug":18,"properties":142,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":145,"statistic":18},[],{"title":143},{"VI":144},"Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China",[],{"id":147,"sortIndex":148,"affiliation":149,"properties":18},"a39f78a0-f19c-48d3-a276-ddca3e10b957",1,{"id":147,"createTime":18,"updateTime":18,"relativeEntities":150,"slug":18,"properties":151,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":154,"statistic":18},[],{"title":152},{"VI":153},"Graduate School of Chinese Academy of Sciences, Beijing, PR China",[],{"title":156,"gsAuthor":158},{"VI":157},"Jie Xiong",{"VOID":159},"[\"6TZzVZkAAAAJ\"]",{"id":161,"sortIndex":148,"researcher":18,"roles":162,"affiliations":163,"properties":185},"7008abaa-2a1f-4629-a282-e66bdcc63f01",[136],[164,170,178],{"id":139,"sortIndex":19,"affiliation":165,"properties":18},{"id":139,"createTime":18,"updateTime":18,"relativeEntities":166,"slug":18,"properties":167,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":169,"statistic":18},[],{"title":168},{"VI":144},[],{"id":171,"sortIndex":148,"affiliation":172,"properties":18},"2f75d229-951e-454b-8702-ab3f418dd99c",{"id":171,"createTime":18,"updateTime":18,"relativeEntities":173,"slug":18,"properties":174,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":177,"statistic":18},[],{"title":175},{"VI":176},"College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, PR China",[],{"id":147,"sortIndex":179,"affiliation":180,"properties":18},2,{"id":147,"createTime":18,"updateTime":18,"relativeEntities":181,"slug":18,"properties":182,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":184,"statistic":18},[],{"title":183},{"VI":153},[],{"title":186,"gsAuthor":188},{"VI":187},"Lifang Feng",{"VOID":189},"[\"xJ_9GaIAAAAJ\"]",{"id":191,"sortIndex":179,"researcher":18,"roles":192,"affiliations":193,"properties":200},"33bdf8f2-9da9-4b1b-9888-2f0c57c31dfe",[136],[194],{"id":139,"sortIndex":19,"affiliation":195,"properties":18},{"id":139,"createTime":18,"updateTime":18,"relativeEntities":196,"slug":18,"properties":197,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":199,"statistic":18},[],{"title":198},{"VI":144},[],{"title":201},{"VI":202},"Dongxia Yuan",{"id":204,"sortIndex":50,"researcher":18,"roles":205,"affiliations":206,"properties":223},"6bce473c-d67e-4359-b380-624d999e078c",[136],[207,215],{"id":208,"sortIndex":19,"affiliation":209,"properties":18},"d91bd9c0-f156-4bef-a172-70f5e3a3703a",{"id":208,"createTime":18,"updateTime":18,"relativeEntities":210,"slug":18,"properties":211,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":214,"statistic":18},[],{"title":212},{"VI":213},"State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China",[],{"id":216,"sortIndex":148,"affiliation":217,"properties":18},"d11db9c0-f5aa-4be4-9c7d-71c07b1bec58",{"id":216,"createTime":18,"updateTime":18,"relativeEntities":218,"slug":18,"properties":219,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":222,"statistic":18},[],{"title":220},{"VI":221},"Program in Systematic Biology, Evolutionary Biology Centre, Uppsala, Sweden",[],{"title":224,"gsAuthor":226},{"VI":225},"Chengjie Fu",{"VOID":227},"[\"KNCgZOEAAAAJ\"]",{"id":229,"sortIndex":56,"researcher":18,"roles":230,"affiliations":231,"properties":238},"390d3ae9-3c85-47f8-bf34-530436bc8075",[136],[232],{"id":139,"sortIndex":19,"affiliation":233,"properties":18},{"id":139,"createTime":18,"updateTime":18,"relativeEntities":234,"slug":18,"properties":235,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":237,"statistic":18},[],{"title":236},{"VI":144},[],{"title":239},{"VI":240},"Wei Miao","ARTICLE",{"url":131,"publisher":243,"properties":262},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":244,"slug":10,"properties":245,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":248,"manageAffiliations":249,"indexDatabases":250,"url":18,"thumbnailPath":18,"statistic":257,"gsStatistic":18,"type":18,"analyzePriority":18},[],{"title":246,"eissn":247},{"EN":13},{"VOID":15},[],[],[251],{"id":24,"indexDatabase":252,"url":35,"indexYears":36,"academicFieldIds":18,"indexDatabaseRanking":37},{"id":26,"createTime":18,"updateTime":18,"relativeEntities":253,"label":254,"description":255,"key":32,"publicationTags":256,"standard":18},[],{"EN":29,"VI":29},{"EN":29,"VI":31},[34],{"impactFactor":19,"impactFactorByYear":258,"i10Index":51,"i10IndexLast5Year":52,"totalPublication":53,"totalPublicationByYear":259,"totalCitation":70,"totalCitationByYear":260,"totalCitationPerPublication":88,"totalCitationPerPublicationByYear":261,"hindexLast5Year":105,"hindex":105},{"2012":40,"2013":41,"2014":42,"2015":43,"2016":44,"2017":45,"2018":46,"2019":47,"2020":48,"2021":49,"2022":50},{"2005":55,"2006":56,"2007":57,"2008":58,"2009":59,"2010":60,"2011":61,"2012":62,"2013":63,"2014":64,"2015":65,"2016":66,"2017":67,"2018":68,"2019":69,"2020":62},{"2005":72,"2006":73,"2007":74,"2008":75,"2009":76,"2010":77,"2011":78,"2012":79,"2013":80,"2014":81,"2015":82,"2016":83,"2017":84,"2018":85,"2019":86,"2020":87},{"2005":90,"2006":91,"2007":92,"2008":93,"2009":94,"2010":95,"2011":96,"2012":97,"2013":98,"2014":52,"2015":99,"2016":100,"2017":101,"2018":102,"2019":103,"2020":104},{"pages":263,"volume":265},{"VOID":264},"1-18",{"VOID":266},"10",{"total":19,"publishYear":268,"statisticByYear":269},2010,{},"2010-10-27","ERROR_IN_ANALYZE_CITATION","2026-08-15T15:04:05.964+00:00",[37],false,{"id":276,"createTime":277,"updateTime":278,"relativeEntities":279,"slug":280,"properties":281,"entityType":127,"verifyStatus":128,"verifyTime":292,"verifyNote":130,"languages":18,"translateLanguages":18,"viewCount":19,"primaryUrl":293,"fullTextUrl":18,"authors":294,"publicationType":241,"publisherRelationship":323,"citationCount":18,"citationInfo":18,"publishDate":348,"publishYear":349,"citationAnalyzeStatus":350,"lastCitationAnalyze":351,"indexDatabases":352,"openAccess":18,"references":18,"isForceReanalyzing":274},"ed14ccda-6f1a-44f9-8172-a77b2dda5ffa","2023-12-09T11:48:09.897+00:00","2026-08-15T12:20:30.415+00:00",[],"One-misdated-sequence-of-rabbit-hemorrhagic-disease-virus-prevents-accurate-estimation-of-its-nucleotide-substitution-rate",{"abstract":282,"title":284,"gsPaper":286,"references":288,"doi":290},{"EN":283},"The literature is ripe with phylogenetic estimates of nucleotide substitution rates, especially of measurably evolving species such as RNA viruses. However, it is not known how robust these rate estimates are to inaccuracies in the data, particularly in sampling dates that are used for molecular clock calibration. Here we report on the rate of evolution of the emerging pathogen Rabbit hemorrhagic disease virus (RHDV), which has significantly different rates of evolution for the same outer capsid (VP60) gene published in the literature. In an attempt to reconcile the conflicting data and further elucidate details of RHDV ’s evolutionary history, we undertook fresh Bayesian analyses and employed jackknife control methods to produce robust substitution rate and time to most recent common ancestor (TMRCA) estimates for RHDV based on the VP60 and RNA-dependent RNA polymerase genes. Through these control methods, we were able to identify a single misdated taxon, a passaged lab strain used for vaccine production, which was responsible for depressing the RHDV capsid gene’s rate of evolution by 65%. Without this isolate, the polymerase and the capsid protein genes had nearly identical rates of evolution: 1.90x10-3 nucleotide substitutions\u002Fsite\u002Fyear, ns\u002Fs\u002Fy, (95% highest probability density (HPD) 1.25x10-3-2.55x10-3) and 1.91x10-3 ns\u002Fs\u002Fy (95% HPD 1.50x10-3-2.34x10-3), respectively. After excluding the misdated taxon, both genes support a significantly higher substitution rate as well as a relatively recent emergence of RHDV, and obviate the need for previously hypothesized decades of unobserved diversification of the virus. The control methods show that using even one misdated taxon in a large dataset can significantly skew estimates of evolutionary parameters and suggest that it is better practice to use smaller datasets composed of taxa with unequivocal isolation dates. These jackknife controls would be useful for future tip-calibrated rate analyses that include taxa with ambiguous dates of isolation.",{"EN":285},"One misdated sequence of rabbit hemorrhagic disease virus prevents accurate estimation of its nucleotide substitution rate",{"VOID":287},"[]",{"VOID":289},"Chen RB, Holmes EC: Avian influenza virus exhibits rapid evolutionary dynamics. Mol Biol Evol. 2006, 23: 2336-2341. 10.1093\u002Fmolbev\u002Fmsl102.\nFourment M, Wood JT, Gibbs AJ, Gibbs MJ: Evolutionary dynamics of the N1 neuraminidases of the main lineages of influenza A viruses. Mol Phylogenet Evol. 2010, 56: 526-535. 10.1016\u002Fj.ympev.2010.04.039.\nSmith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, et al: Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature. 2009, 459: 1122-1126. 10.1038\u002Fnature08182.\nDavid D, Hughes GJ, Yakobson BA, Davidson I, Un H, Aylan O, Kuzmin IV, Rupprecht CE: Identification of novel canine rabies virus clades in the Middle East and North Africa. J Gen Virol. 2007, 88: 967-980. 10.1099\u002Fvir.0.82352-0.\nDavis PL, Bourhy H, Holmes EC: The evolutionary history and dynamics of bat rabies virus. Infect Genet Evol. 2006, 6: 464-473. 10.1016\u002Fj.meegid.2006.02.007.\nBourhy H, Reynes JM, Dunham EJ, Dacheux L, Larrous F, Huong VTO, Xu GL, Yan JX, Miranda MEG, Holmes EC: The origin and phylogeography of dog rabies virus. J Gen Virol. 2008, 89: 2673-2681. 10.1099\u002Fvir.0.2008\u002F003913-0.\nTalbi C, Holmes EC, De Benedictis P, Faye O, Nakoune E, Gamatie D, Diarra A, Elmamy BO, Sow A, Adjogoua EV, et al: Evolutionary history and dynamics of dog rabies virus in western and central Africa. J Gen Virol. 2009, 90: 783-791. 10.1099\u002Fvir.0.007765-0.\nMing PG, Yan JX, Rayner S, Meng SL, Xu GL, Tang Q, Wu J, Luo J, Yang XM: A history estimate and evolutionary analysis of rabies virus variants in China. J Gen Virol. 2010, 91: 759-764. 10.1099\u002Fvir.0.016436-0.\nAlda F, Gaitero T, Suarez M, Merchan T, Rocha G, Doadrio I: Evolutionary history and molecular epidemiology of rabbit haemorrhagic disease virus in the Iberian Peninsula and Western Europe. BMC Evol Biol. 2010, 10: 347-10.1186\u002F1471-2148-10-347.\nJahnke M, Holmes EC, Kerr PJ, Wright JD, Strive T: Evolution and phylogeography of the nonpathogenic calicivirus RCV-A1 in wild rabbits in Australia. J Virol. 2010, 84: 12397-12404. 10.1128\u002FJVI.00777-10.\nJenkins GM, Rambaut A, Pybus OG, Holmes EC: Rates of molecular evolution in RNA viruses: A quantitative phylogenetic analysis. J Mol Evol. 2002, 54: 156-165. 10.1007\u002Fs00239-001-0064-3.\nKerr PJ, Kitchen A, Holmes EC: Origin and phylodynamics of rabbit hemorrhagic disease virus. J Virol. 2009, 83: 12129-12138. 10.1128\u002FJVI.01523-09.\nKinnear M, Linde CC: Capsid gene divergence in rabbit hemorrhagic disease virus. J Gen Virol. 2010, 91: 174-181. 10.1099\u002Fvir.0.014076-0.\nForrester NL, Trout RC, Turner SL, Kelly D, Boag B, Moss S, Gould EA: Unravelling the paradox of rabbit haemorrhagic disease virus emergence, using phylogenetic analysis; possible implications for rabbit conservation strategies. Biol Conserv. 2006, 131: 296-306. 10.1016\u002Fj.biocon.2006.05.005.\nForrester NL, Abubakr ML, Abu Elzein EME, al-Afaleq AL, Housawi FMT, Moss SR, Turner SL, Gould EA: Phylogenetic analysis of rabbit haemorrhagic disease virus strains from the Arabian Peninsula: Did RHDV emerge simultaneously in Europe and Asia?. Virology. 2006, 544 (344): 277-282.\nCooke BD: Rabbit haemorrhagic disease: field epidemiology and the management of wild rabbit populations. Rev Sci Tech Oie. 2002, 21: 347-358.\nMcIntosh MT, Behan SC, Mohamed FM, Lu ZQ, Moran KE, Burrage TG, Neilan JG, Ward GB, Botti G, Capucci L, Metwally SA: A pandemic strain of calicivirus threatens rabbit industries in the Americas. Virol J. 2007, 4: 96-10.1186\u002F1743-422X-4-96.\nSaunders G, Kay B, Mutze G, Choquenot D: Observations on the impacts of rabbit haemorrhagic disease on agricultural production values in Australia. Wildlife Res. 2002, 29: 605-613. 10.1071\u002FWR00086.\nDelibes-Mateos M, Redpath SM, Angulo E, Ferrerasa P, Villafuerte R: Rabbits as a keystone species in southern Europe. Biol Conserv. 2007, 137: 149-156. 10.1016\u002Fj.biocon.2007.01.024.\nParkes JP, Norbury GL, Heyward RP, Sullivan G: Epidemiology of rabbit haemorrhagic disease (RHD) in the South Island, New Zealand, 1997-2001. Wildlife Res. 2002, 29: 543-555. 10.1071\u002FWR00108.\nBergin IL, Wise AG, Bolin SR, Mullaney TP, Kiupel M, Maes RK: Novel Calicivirus Identified in Rabbits, Michigan, USA. Emerg Infect Dis. 2009, 15: 1955-1962.\nCapucci L, Fusi P, Lavazza A, Pacciarini ML, Rossi C: Detection and preliminary characterization of a new rabbit calicivirus related to rabbit hemorrhagic disease virus but nonpathogenic. J Virol. 1996, 70: 8614-8623.\nForrester NL, Trout RC, Gould EA: Benign circulation of rabbit haemorrhagic disease virus on Lambay Island, Eire. Virology. 2007, 358: 18-22. 10.1016\u002Fj.virol.2006.09.011.\nStrive T, Wright JD, Robinson AJ: Identification and partial characterisation of a new lagovirus in Australian wild rabbits. Virology. 2009, 384: 97-105. 10.1016\u002Fj.virol.2008.11.004.\nMoss SR, Turner SL, Trout RC, White PJ, Hudson PJ, Desai A, Armesto M, Forrester NL, Gould EA: Molecular epidemiology of rabbit haemorrhagic disease virus. J Gen Virol. 2002, 83: 2461-2467.\nWalsh PD, Biek R, Real LA: Wave-like spread of Ebola Zaire. Plos Biol. 2005, 3: 1946-1953.\nVijaykrishna D, Smith GJD, Zhang JX, Peiris JSM, Chen H, Guan Y: Evolutionary insights into the ecology of coronaviruses. J Virol. 2007, 81: 4012-4020. 10.1128\u002FJVI.02605-06.\nSmith GJD, Bahl J, Vijaykrishna D, Zhang JX, Poon LLM, Chen HL, Webster RG, Peiris JSM, Guan Y: Dating the emergence of pandemic influenza viruses. P Natl Acad Sci USA. 2009, 106: 11709-11712. 10.1073\u002Fpnas.0904991106.\nBok K, Abente EJ, Realpe-Quintero M, Mitra T, Sosnovtsev SV, Kapikian AZ, Green KY: Evolutionary Dynamics of GII.4 Noroviruses over a 34- Year Period. J Virol. 2009, 83: 11890-11901. 10.1128\u002FJVI.00864-09.\nShi M, Lam TTY, Hon CC, Murtaugh MP, Davies PR, Hui RKH, Li J, Wong LTW, Yip CW, Jiang JW, Leung FCC: Phylogeny-Based Evolutionary, Demographical, and Geographical Dissection of North American Type 2 Porcine Reproductive and Respiratory Syndrome Viruses. J Virol. 2010, 84: 8700-8711. 10.1128\u002FJVI.02551-09.\nHanada K, Suzuki Y, Nakane T, Hirose O, Gojobori T: The origin and evolution of porcine reproductive and respiratory syndrome viruses. Mol Biol Evol. 2005, 22: 1024-1031. 10.1093\u002Fmolbev\u002Fmsi089.\nPeacock D, Mutze G, Sinclair R, Kovaliski J, Cooke B: Rabbit haemorrhagic disease: Applying Occam's razor to competing hypotheses. Mol Ecol. 2012, 21: 1038-1041. 10.1111\u002Fj.1365-294X.2011.05466.x.\nGould EA: First case of rabbit haemorrhagic disease in Canada: contaminated flying insect, vs. long-term infection hypothesis. Mol Ecol. 2012, 21: 1042-1047. 10.1111\u002Fj.1365-294X.2012.05462.x.\nHeath TA, Hedtke SM, Hillis DM: Taxon sampling and the accuracy of phylogenetic analyses. J Syst Evol. 2008, 46: 239-257.\nHo SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A: Time-dependent rates of molecular evolution. Mol Ecol. 2011, 20: 3087-3101. 10.1111\u002Fj.1365-294X.2011.05178.x.\nRobinson M, Gouy M, Gautier C, Mouchiroud D: Sensitivity of the relative-rate test to taxonomic sampling. Mol Biol Evol. 1998, 15: 1091-1098. 10.1093\u002Foxfordjournals.molbev.a026016.\nForrester NL, Moss SR, Turner SL, Schirrmeier H, Gould EA: Recombination in rabbit haemorrhagic disease virus: Possible impact on evolution and epidemiology. Virology. 2008, 376: 390-396. 10.1016\u002Fj.virol.2008.03.023.\nEsteves PJ, Abrantes J, Carneiro M, Muller A, Thompson G, van der Loo W: Detection of positive selection in the major capsid protein VP60 of the rabbit haemorrhagic disease virus (RHDV). Virus Res. 2008, 137: 253-256. 10.1016\u002Fj.virusres.2008.07.025.\nOem JK, Lee KN, Roh IS, Lee KK, Kim SH, Kim HR, Park CK, Joo YS: Identification and characterization of rabbit hemorrhagic disease virus genetic variants isolated in Korea. J Vet Med Sci. 2009, 71: 1519-1523. 10.1292\u002Fjvms.001519.\nWertheim JO: The re-emergence of H1N1 Influenza virus in 1977: A cautionary tale for estimating divergence times using biologically unrealistic sampling dates. PLoS One. 2010, 5 (6): 11184-10.1371\u002Fjournal.pone.0011184.\nRamsden C, Holmes EC, Charleston MA: Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence. Mol Biol Evol. 2009, 26: 143-153.\nHo SYW, Phillips MJ, Cooper A, Drummond AJ: Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 2005, 22: 1561-1568. 10.1093\u002Fmolbev\u002Fmsi145.\nFirth C, Kitchen A, Shapiro B, Suchard MA, Holmes EC, Rambaut A: Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses. Mol Biol Evol. 2010, 27: 2038-2051. 10.1093\u002Fmolbev\u002Fmsq088.\nSiddall ME: Another monophyly index: Revisiting the jackknife. Cladistics. 1995, 11: 33-56. 10.1111\u002Fj.1096-0031.1995.tb00003.x.\nLanyon SM: Detecting Internal Inconsistencies in Distance Data. Syst Zool. 1985, 34: 397-403. 10.2307\u002F2413204.\nLapointe FJ, Kirsch JAW, Bleiweiss R: Jackknifing of Weighted Trees - Validation of Phylogenies Reconstructed from Distance Matrices. Mol Phylogenet Evol. 1994, 3: 256-267. 10.1006\u002Fmpev.1994.1028.\nThorley JL, Wilkinson M: Testing the phylogenetic stability of early tetrapods. J Theor Biol. 1999, 200: 343-344. 10.1006\u002Fjtbi.1999.0999.\nMariadassou M, Bar-Hen A, Kishino H: Taxon influence index: assessing taxon-induced incongruities in phylogenetic inference. Syst Biol. 2012, 61: 337-345. 10.1093\u002Fsysbio\u002Fsyr129.\nWang YS, Lu CP, Zhou ZA: High expression of the capsid protein gene of the Chinese early isolate NJ85 of rabbit hemorrhagic disease virus in Escherichia coli. Journal of Agricultural Biotechnology. 2004, 12: 408-411.\nWang F, Hu B, Ren X, Fan Z, Yang L, Xu W, Zhang Z, He K: Expression of the capsid protein of rabbit haemorrhagic disease virus in insect cells and its protective efficacy to rabbits. Chinese Journal of Animal and Veterinary Sciences. 2010, 39: 1382-1387.\nNikolaev AV: New strains of rabbit haemorrhagic disease virus in Russia. Veterinary Medicine Journal. 2011, 2: 25-28.\nHarkins GW, Delport W, Duffy S, Wood N, Monjane AL, Owor BE, Donaldson L, Saumtally S, Triton G, Briddon RW, et al: Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts. Virol J. 2009, 6: 104-10.1186\u002F1743-422X-6-104.\nPybus OG, Barnes E, Taggart R, Lemey P, Markov PV, Rasachak B, Syhavong B, Phetsouvanah R, Sheridan I, Humphreys IS, et al: Genetic History of Hepatitis C Virus in East Asia. J Virol. 2009, 83: 1071-1082. 10.1128\u002FJVI.01501-08.\nAraujo JMG, Nogueira RMR, Schatzmayr HG, Zanotto PMD, Bello G: Phylogeography and evolutionary history of dengue virus type 3. Infect Genet Evol. 2009, 9: 716-725. 10.1016\u002Fj.meegid.2008.10.005.\nFaria NR, de Vries M, van Hemert FJ, Benschop K, van der Hoek L: Rooting human parechovirus evolution in time. BMC Evol Biol. 2009, 9: 164-10.1186\u002F1471-2148-9-164.\nAuguste AJ, Pybus OG, Carrington CVF: Evolution and dispersal of St. Louis encephalitis virus in the Americas. Infect Genet Evol. 2009, 9: 709-715. 10.1016\u002Fj.meegid.2008.07.006.\nArrigo NC, Adams AP, Weaver SC: Evolutionary Patterns of Eastern Equine Encephalitis Virus in North versus South America Suggest Ecological Differences and Taxonomic Revision. J Virol. 2010, 84: 1014-1025. 10.1128\u002FJVI.01586-09.\nAnez G, Morales-Betoulle ME, Rios M: Circulation of Different Lineages of Dengue Virus Type 2 in Central America, Their Evolutionary Time-Scale and Selection Pressure Analysis. PLoS One. 2011, 6 (11): 27459-10.1371\u002Fjournal.pone.0027459.\nSall AA, Faye O, Diallo M, Firth C, Kitchen A, Holmes EC: Yellow Fever Virus Exhibits Slower Evolutionary Dynamics than Dengue Virus. J Virol. 2010, 84: 765-772. 10.1128\u002FJVI.01738-09.\nHicks AL, Duffy S: Genus-Specific Substitution Rate Variability among Picornaviruses. J Virol. 2011, 85: 7942-7947. 10.1128\u002FJVI.02535-10.\nRambaut A: Se-Al: Sequence alignment editor. Version 2.0a11. 2002, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK\nMartin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P: RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics. 2010, 26: 2462-2463. 10.1093\u002Fbioinformatics\u002Fbtq467.\nPosada D, Crandall KA: MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998, 14: 817-818. 10.1093\u002Fbioinformatics\u002F14.9.817.\nDrummond AJ, Rambaut A: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007, 7: 214-10.1186\u002F1471-2148-7-214.\nRambaut A, Drummond AJ: Tracer: MCMC Trace Analysis Tool. Version 1.5. 2007, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK\nSwofford DL: PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4.0b10. 2003, Sinauer Associates, Sunderland, MA\nDuffy S, Holmes EC: Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J Gen Virol. 2009, 90: 1539-1547. 10.1099\u002Fvir.0.009266-0.\nRambaut A: Path-O-Gen: Temporal Signal Investigation Tool. Version 1.3. 2010, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK\nR Development Core Team: R: A Language and Environment for Statistical Computing. Version 2.14.1. 2011, R Foundation for Statistical Computing, Vienna, AT\nMajeed R: violinmplot: Combination of violin plot with mean and standard deviation. 2010, http:\u002F\u002Fcran.r-project.org\u002Fweb\u002Fpackages\u002Fviolinmplot\u002Fviolinmplot.pdf,\nShapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus OG, Rambaut A: A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages. Mol Biol Evol. 2011, 28: 879-887. 10.1093\u002Fmolbev\u002Fmsq262.",{"VOID":291},"10.1186\u002F1471-2148-12-74","2024-09-04T20:56:12.420+00:00","http:\u002F\u002Fbmcevolbiol.biomedcentral.com\u002Farticles\u002F10.1186\u002F1471-2148-12-74",[295,310],{"id":296,"sortIndex":19,"researcher":18,"roles":297,"affiliations":298,"properties":307},"17c0fef2-8275-4f25-a26b-a7cd4eec30d9",[136],[299],{"id":300,"sortIndex":19,"affiliation":301,"properties":18},"30a8153b-ab48-4311-bf7a-239bd8eea02a",{"id":300,"createTime":18,"updateTime":18,"relativeEntities":302,"slug":18,"properties":303,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":306,"statistic":18},[],{"title":304},{"VI":305},"Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers the State University of New Jersey, New Brunswick, USA",[],{"title":308},{"VI":309},"Allison L Hicks",{"id":311,"sortIndex":148,"researcher":18,"roles":312,"affiliations":313,"properties":320},"04f37055-fa8a-47ef-846d-cc211b728392",[136],[314],{"id":300,"sortIndex":19,"affiliation":315,"properties":18},{"id":300,"createTime":18,"updateTime":18,"relativeEntities":316,"slug":18,"properties":317,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":319,"statistic":18},[],{"title":318},{"VI":305},[],{"title":321},{"VI":322},"Siobain Duffy",{"url":293,"publisher":324,"properties":343},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":325,"slug":10,"properties":326,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":329,"manageAffiliations":330,"indexDatabases":331,"url":18,"thumbnailPath":18,"statistic":338,"gsStatistic":18,"type":18,"analyzePriority":18},[],{"title":327,"eissn":328},{"EN":13},{"VOID":15},[],[],[332],{"id":24,"indexDatabase":333,"url":35,"indexYears":36,"academicFieldIds":18,"indexDatabaseRanking":37},{"id":26,"createTime":18,"updateTime":18,"relativeEntities":334,"label":335,"description":336,"key":32,"publicationTags":337,"standard":18},[],{"EN":29,"VI":29},{"EN":29,"VI":31},[34],{"impactFactor":19,"impactFactorByYear":339,"i10Index":51,"i10IndexLast5Year":52,"totalPublication":53,"totalPublicationByYear":340,"totalCitation":70,"totalCitationByYear":341,"totalCitationPerPublication":88,"totalCitationPerPublicationByYear":342,"hindexLast5Year":105,"hindex":105},{"2012":40,"2013":41,"2014":42,"2015":43,"2016":44,"2017":45,"2018":46,"2019":47,"2020":48,"2021":49,"2022":50},{"2005":55,"2006":56,"2007":57,"2008":58,"2009":59,"2010":60,"2011":61,"2012":62,"2013":63,"2014":64,"2015":65,"2016":66,"2017":67,"2018":68,"2019":69,"2020":62},{"2005":72,"2006":73,"2007":74,"2008":75,"2009":76,"2010":77,"2011":78,"2012":79,"2013":80,"2014":81,"2015":82,"2016":83,"2017":84,"2018":85,"2019":86,"2020":87},{"2005":90,"2006":91,"2007":92,"2008":93,"2009":94,"2010":95,"2011":96,"2012":97,"2013":98,"2014":52,"2015":99,"2016":100,"2017":101,"2018":102,"2019":103,"2020":104},{"pages":344,"volume":346},{"VOID":345},"1-12",{"VOID":347},"12","2012-05-30",2012,"ERROR_IN_GET_PLATFORM_ID","2026-08-15T12:20:30.414+00:00",[37],{"id":354,"createTime":355,"updateTime":356,"relativeEntities":357,"slug":358,"properties":359,"entityType":127,"verifyStatus":128,"verifyTime":373,"verifyNote":130,"languages":374,"translateLanguages":18,"viewCount":19,"primaryUrl":376,"fullTextUrl":18,"authors":377,"publicationType":241,"publisherRelationship":615,"citationCount":635,"citationInfo":636,"publishDate":639,"publishYear":637,"citationAnalyzeStatus":350,"lastCitationAnalyze":640,"indexDatabases":641,"openAccess":18,"references":642,"isForceReanalyzing":274},"917228f5-5dcd-4315-8156-7640046a8d65","2024-04-14T23:55:05.338+00:00","2026-07-29T00:12:42.262+00:00",[],"Tracing-the-colonization-history-of-the-Indian-Ocean-scops-owls-Strigiformes-Otus-with-further-insight-into-the-spatio-temporal-origin-of-the-Malagasy-avifauna",{"mag":360,"gsPaper":362,"pmc":363,"openalex":365,"title":367,"pm":369,"doi":371},{"VOID":361},"2143748885",{"VOID":287},{"VOID":364},"2483963",{"VOID":366},"W2143748885",{"EN":368},"Tracing the colonization history of the Indian Ocean scops-owls (Strigiformes: Otus) with further insight into the spatio-temporal origin of the Malagasy avifauna",{"VOID":370},"18611281",{"VOID":372},"10.1186\u002F1471-2148-8-197","2024-06-25T02:05:06.624+00:00",[375],"EN","http:\u002F\u002Fbmcevolbiol.biomedcentral.com\u002Farticles\u002F10.1186\u002F1471-2148-8-197",[378,397,412,431,450,469,489,507,524,544,560,578,597],{"id":379,"sortIndex":19,"researcher":18,"roles":380,"affiliations":381,"properties":390},"89e06462-8538-4d8d-b13c-f65ed676c614",[],[382],{"id":383,"sortIndex":19,"affiliation":384,"properties":18},"db3cce70-396c-4146-96bb-169d5438b47e",{"id":383,"createTime":18,"updateTime":18,"relativeEntities":385,"slug":18,"properties":386,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":389,"statistic":18},[],{"title":387},{"EN":388},"UMR5202 «Origine, Structure et Evolution de la Biodiversité», Département Systématique et Evolution, Muséum National d'Histoire Naturelle, 55 Rue Buffon, 75005, Paris, France",[],{"orcid":391,"title":393,"openalex":395},{"VOID":392},"https:\u002F\u002Forcid.org\u002F0000-0003-1972-0078",{"EN":394},"Jérôme Fuchs",{"VOID":396},"A5035058135",{"id":398,"sortIndex":148,"researcher":18,"roles":399,"affiliations":400,"properties":407},"ad8ee94f-1f10-4214-b784-c157d4d23207",[],[401],{"id":383,"sortIndex":19,"affiliation":402,"properties":18},{"id":383,"createTime":18,"updateTime":18,"relativeEntities":403,"slug":18,"properties":404,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":406,"statistic":18},[],{"title":405},{"EN":388},[],{"title":408,"openalex":410},{"EN":409},"Jean‐Marc Pons",{"VOID":411},"A5028977264",{"id":413,"sortIndex":179,"researcher":18,"roles":414,"affiliations":415,"properties":424},"cd7aeb3a-c119-4a9f-8611-0ef401b7892c",[],[416],{"id":417,"sortIndex":19,"affiliation":418,"properties":18},"ab04f2b2-4952-412c-8de0-885b8f5943fe",{"id":417,"createTime":18,"updateTime":18,"relativeEntities":419,"slug":18,"properties":420,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":423,"statistic":18},[],{"title":421},{"VI":422},"Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA",[],{"orcid":425,"title":427,"openalex":429},{"VOID":426},"https:\u002F\u002Forcid.org\u002F0000-0001-9318-0570",{"EN":428},"Steven M. Goodman",{"VOID":430},"A5014534741",{"id":432,"sortIndex":50,"researcher":18,"roles":433,"affiliations":434,"properties":443},"16f6179c-faf0-4eca-9ec9-07e6f89bd335",[],[435],{"id":436,"sortIndex":19,"affiliation":437,"properties":18},"0f957424-284b-47a4-a66a-7bd2fb65386e",{"id":436,"createTime":18,"updateTime":18,"relativeEntities":438,"slug":18,"properties":439,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":442,"statistic":18},[],{"title":440},{"EN":441},"CEBC-CNRS, Beauvoir sur Niort, 79360, France",[],{"orcid":444,"title":446,"openalex":448},{"VOID":445},"https:\u002F\u002Forcid.org\u002F0000-0002-2320-7755",{"EN":447},"Vincent Bretagnolle",{"VOID":449},"A5011716970",{"id":451,"sortIndex":56,"researcher":18,"roles":452,"affiliations":453,"properties":462},"024100a2-d93d-4296-b8c6-2b154c03142c",[],[454],{"id":455,"sortIndex":19,"affiliation":456,"properties":18},"d5ba8c29-ccb1-4cc9-bd7d-b48c1d1a93e1",{"id":455,"createTime":18,"updateTime":18,"relativeEntities":457,"slug":18,"properties":458,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":461,"statistic":18},[],{"title":459},{"EN":460},"UMR5175 Centre d'Ecologie Fonctionnelle et Evolutive, 1919 Route de Mende, F-34293, Montpellier Cedex 5, France",[],{"orcid":463,"title":465,"openalex":467},{"VOID":464},"https:\u002F\u002Forcid.org\u002F0000-0003-1394-4361",{"EN":466},"Martim Melo",{"VOID":468},"A5079110975",{"id":470,"sortIndex":471,"researcher":18,"roles":472,"affiliations":473,"properties":482},"55f958ba-6104-4711-bf98-a67d436f7ab7",5,[],[474],{"id":475,"sortIndex":19,"affiliation":476,"properties":18},"c27d5db9-dab3-46e8-b0af-bcbcc1cd89d3",{"id":475,"createTime":18,"updateTime":18,"relativeEntities":477,"slug":18,"properties":478,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":481,"statistic":18},[],{"title":479},{"EN":480},"Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, 3101 Valley Life Science Building, Berkeley, CA, 94720-3160, USA",[],{"orcid":483,"title":485,"openalex":487},{"VOID":484},"https:\u002F\u002Forcid.org\u002F0000-0001-8328-6021",{"EN":486},"Rauri C. K. Bowie",{"VOID":488},"A5019980281",{"id":490,"sortIndex":491,"researcher":18,"roles":492,"affiliations":493,"properties":502},"dfc0b8e2-8efd-48e3-93a5-c50771d7ae26",6,[],[494],{"id":495,"sortIndex":19,"affiliation":496,"properties":18},"1fc3fbeb-df0e-41b3-a9ce-87fa2fd8f1b8",{"id":495,"createTime":18,"updateTime":18,"relativeEntities":497,"slug":18,"properties":498,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":501,"statistic":18},[],{"title":499},{"EN":500},"Nature Seychelles, PO Box 1310, Victoria, Mahé, Republic of Seychelles",[],{"title":503,"openalex":505},{"EN":504},"David J. Currie",{"VOID":506},"A5040390464",{"id":508,"sortIndex":55,"researcher":18,"roles":509,"affiliations":510,"properties":519},"676c7ea0-7b0c-4482-aa57-300879335035",[],[511],{"id":512,"sortIndex":19,"affiliation":513,"properties":18},"567069c7-d84f-4309-b10f-e95caa74c25b",{"id":512,"createTime":18,"updateTime":18,"relativeEntities":514,"slug":18,"properties":515,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":518,"statistic":18},[],{"title":516},{"VI":517},"BirdLife International, Wellbrook Court, Girton Road, Cambridge CB3 0NA, UK",[],{"title":520,"openalex":522},{"EN":521},"Roger Safford",{"VOID":523},"A5037499099",{"id":525,"sortIndex":526,"researcher":18,"roles":527,"affiliations":528,"properties":537},"763973a7-8f59-4355-a845-4217baaa4851",8,[],[529],{"id":530,"sortIndex":19,"affiliation":531,"properties":18},"07d08161-79b3-4863-a8f6-61e12d924bab",{"id":530,"createTime":18,"updateTime":18,"relativeEntities":532,"slug":18,"properties":533,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":536,"statistic":18},[],{"title":534},{"EN":535},"The Peregrine Fund, 5668 West Flying Hawk Lane, Boise Idaho, 83709, USA",[],{"orcid":538,"title":540,"openalex":542},{"VOID":539},"https:\u002F\u002Forcid.org\u002F0000-0002-3728-6677",{"EN":541},"Munir Z. Virani",{"VOID":543},"A5027157752",{"id":545,"sortIndex":546,"researcher":18,"roles":547,"affiliations":548,"properties":555},"41f827ff-1ee6-4761-86e8-eb08726b7df5",9,[],[549],{"id":530,"sortIndex":19,"affiliation":550,"properties":18},{"id":530,"createTime":18,"updateTime":18,"relativeEntities":551,"slug":18,"properties":552,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":554,"statistic":18},[],{"title":553},{"EN":535},[],{"title":556,"openalex":558},{"EN":557},"Simon Thomsett",{"VOID":559},"A5031861418",{"id":561,"sortIndex":562,"researcher":18,"roles":563,"affiliations":564,"properties":573},"f5dbc344-12a8-4a54-9445-46245c43c890",10,[],[565],{"id":566,"sortIndex":19,"affiliation":567,"properties":18},"d56471c7-e53a-446b-ac9e-4840de37002d",{"id":566,"createTime":18,"updateTime":18,"relativeEntities":568,"slug":18,"properties":569,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":572,"statistic":18},[],{"title":570},{"EN":571},"Department of Environment, Ministry of Agriculture, Natural Resources, Environment and Cooperatives, Zanzibar Revolutionary Government, P.O. Box 811, Zanzibar, United Republic of Tanzania",[],{"title":574,"openalex":576},{"EN":575},"A Hija",{"VOID":577},"A5005405784",{"id":579,"sortIndex":57,"researcher":18,"roles":580,"affiliations":581,"properties":590},"308da835-9d31-456e-80e0-0d7f2f7d90e9",[],[582],{"id":583,"sortIndex":19,"affiliation":584,"properties":18},"1e04dd9a-7084-4fc2-985c-2bd9d5006bda",{"id":583,"createTime":18,"updateTime":18,"relativeEntities":585,"slug":18,"properties":586,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":589,"statistic":18},[],{"title":587},{"VI":588},"Genoscope, Centre National de Séquençage, 2, rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France",[],{"orcid":591,"title":593,"openalex":595},{"VOID":592},"https:\u002F\u002Forcid.org\u002F0000-0002-4752-7278",{"EN":594},"Corinne Cruaud",{"VOID":596},"A5051923416",{"id":598,"sortIndex":599,"researcher":18,"roles":600,"affiliations":601,"properties":610},"c937c6ce-4051-4c57-afa6-343b33440047",12,[],[602],{"id":603,"sortIndex":19,"affiliation":604,"properties":18},"70f4ae01-aea5-4f21-bd49-a6518f720f30",{"id":603,"createTime":18,"updateTime":18,"relativeEntities":605,"slug":18,"properties":606,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":609,"statistic":18},[],{"title":607},{"VI":608},"Service Commun de Systématique Moléculaire, IFR CNRS 101, Muséum National d’Histoire Naturelle, 43 rue Cuvier, 75005 Paris, France",[],{"title":611,"openalex":613},{"EN":612},"Éric Pasquet",{"VOID":614},"A5057030024",{"url":18,"publisher":616,"properties":18},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":617,"slug":10,"properties":618,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":621,"manageAffiliations":622,"indexDatabases":623,"url":18,"thumbnailPath":18,"statistic":630,"gsStatistic":18,"type":18,"analyzePriority":18},[],{"title":619,"eissn":620},{"EN":13},{"VOID":15},[],[],[624],{"id":24,"indexDatabase":625,"url":35,"indexYears":36,"academicFieldIds":18,"indexDatabaseRanking":37},{"id":26,"createTime":18,"updateTime":18,"relativeEntities":626,"label":627,"description":628,"key":32,"publicationTags":629,"standard":18},[],{"EN":29,"VI":29},{"EN":29,"VI":31},[34],{"impactFactor":19,"impactFactorByYear":631,"i10Index":51,"i10IndexLast5Year":52,"totalPublication":53,"totalPublicationByYear":632,"totalCitation":70,"totalCitationByYear":633,"totalCitationPerPublication":88,"totalCitationPerPublicationByYear":634,"hindexLast5Year":105,"hindex":105},{"2012":40,"2013":41,"2014":42,"2015":43,"2016":44,"2017":45,"2018":46,"2019":47,"2020":48,"2021":49,"2022":50},{"2005":55,"2006":56,"2007":57,"2008":58,"2009":59,"2010":60,"2011":61,"2012":62,"2013":63,"2014":64,"2015":65,"2016":66,"2017":67,"2018":68,"2019":69,"2020":62},{"2005":72,"2006":73,"2007":74,"2008":75,"2009":76,"2010":77,"2011":78,"2012":79,"2013":80,"2014":81,"2015":82,"2016":83,"2017":84,"2018":85,"2019":86,"2020":87},{"2005":90,"2006":91,"2007":92,"2008":93,"2009":94,"2010":95,"2011":96,"2012":97,"2013":98,"2014":52,"2015":99,"2016":100,"2017":101,"2018":102,"2019":103,"2020":104},48,{"total":635,"publishYear":637,"statisticByYear":638},2008,{"2012":491,"2013":491,"2014":148,"2015":179,"2016":50,"2017":471,"2018":50,"2021":148,"2022":50,"2023":546},"2008-01-01","2026-07-29T00:12:42.261+00:00",[37],[],{"id":644,"createTime":645,"updateTime":646,"relativeEntities":647,"slug":648,"properties":649,"entityType":127,"verifyStatus":128,"verifyTime":660,"verifyNote":130,"languages":18,"translateLanguages":18,"viewCount":19,"primaryUrl":661,"fullTextUrl":18,"authors":662,"publicationType":241,"publisherRelationship":680,"citationCount":19,"citationInfo":705,"publishDate":708,"publishYear":706,"citationAnalyzeStatus":709,"lastCitationAnalyze":646,"indexDatabases":710,"openAccess":18,"references":18,"isForceReanalyzing":274},"a2c9f66c-c080-450f-8156-8f72936593ff","2023-12-11T06:30:47.540+00:00","2026-07-28T21:51:10.608+00:00",[],"Comparative-mitochondrial-genomics-within-and-among-species-of-killifish",{"abstract":650,"title":652,"gsPaper":654,"references":656,"doi":658},{"EN":651},"This study was motivated by the observation of unusual mitochondrial haplotype distributions and associated physiological differences between populations of the killifish Fundulus heteroclitus distributed along the Atlantic coast of North America. A distinct \"northern\" haplotype is fixed in all populations north of New Jersey, and does not appear south of New Jersey except in extreme upper-estuary fresh water habitats, and northern individuals are known to be more tolerant of hyposmotic conditions than southern individuals. Complete mitochondrial genomes were sequenced from individuals from northern coastal, southern coastal, and fresh water populations (and from out-groups). Comparative genomics approaches were used to test multiple evolutionary hypotheses proposed to explain among-population genome variation including directional selection and hybridization. Structure and organization of the Fundulus mitochondrial genome is typical of animals, yet subtle differences in substitution patterns exist among populations. No signals of directional selection or hybridization were detected. Mitochondrial genes evolve at variable rates, but all genes exhibit very low dN\u002FdS ratios across all lineages, and the southern population harbors more synonymous polymorphism than other populations. Evolution of mitochondrial genomes within Fundulus is primarily governed by interaction between strong purifying selection and demographic influences, including larger historical population size in the south. Though directional selection and hybridization hypotheses were not supported, adaptive processes may indirectly contribute to partitioning of variation between populations.",{"EN":653},"Comparative mitochondrial genomics within and among species of killifish",{"VOID":655},"[\"4570967839969763448\"]",{"VOID":657},"Wood CM, Marshall WS: Ion balance, acid-base regulation, and chloride cell function in the Common Killifish, Fundulus heteroclitus – a euryhaline estuarine teleost. Estuaries. 1994, 17 (1A): 34-52. 10.2307\u002F1352333.\nPowers DA, Smith M, Gonzalez-Villasenor I, DiMichelle L, Crawford DL, Bernardi G, Lauerman T: A multidisciplinary approach to the selectionist\u002Fneutralist controversy using the model teleost, Fundulus heteroclitus. Oxford Surveys in Evolutionary Biology. Edited by: Futuyma D, Antonovics J. 1993, New York, NY: Oxford University Press, 9: 43-108.\nBurnett KG, Bain LJ, Baldwin WS, Callard GV, Cohen S, Di Giulio RT, Evans DH, Gómez-Chiarri M, Hahn ME, Hoover CA, et al: Fundulus as the premier teleost model in environmental biology: Opportunities for new insights using genomics. Comp Biochem Physiol Part D Genomics Proteomics. 2007, 2 (4): 257-286. 10.1016\u002Fj.cbd.2007.09.001.\nSmith MW, Chapman RW, Powers DA: Mitochondrial DNA analysis of Atlantic Coast, Chesapeake Bay, and Delaware Bay populations of the teleost Fundulus heteroclitus indicates temporally unstable distributions over geologic time. Mol Mar Biol Biotech. 1998, 7 (2): 79-87.\nAble KW, Palmer RE: Salinity effects on fertilization success and larval mortality of Fundulus heteroclitus. Copeia. 1988, 345-350. 10.2307\u002F1445874. 2,\nScott GR, Rogers JT, Richards JG, Wood CA, Schulte PM: Intraspecific divergence of ionoregulatory physiology in the euryhaline teleost Fundulus heteroclitus: possible mechanisms of freshwater adaptation. J Exp Biol. 2004, 207 (19): 3399-3410. 10.1242\u002Fjeb.01130.\nBernardi G, Sordino P, Powers DA: Concordant Mitochondrial and Nuclear-DNA Phylogenies for Populations of the Teleost Fish Fundulus-Heteroclitus. P Natl Acad Sci USA. 1993, 90 (20): 9271-9274. 10.1073\u002Fpnas.90.20.9271.\nGonzalez-Villasenor LI, Powers DA: Mitochondrial DNA restriction site polymorphisms in the teleost Fundulus heteroclitus support secondary intergradation. Evolution. 1990, 44 (1): 27-37. 10.2307\u002F2409522.\nRopson IJ, Brown DC, Powers DA: Biochemical genetics of Fundulus heteroclitus (L) .6. Geographical variation in the gene frequencies of 15 loci. Evolution. 1990, 44 (1): 16-26. 10.2307\u002F2409521.\nAdams SM, Lindmeier JB, Duvernell DD: Microsatellite analysis of the phylogeography, Pleistocene history and secondary contact hypotheses for the killifish, Fundulus heteroclitus. Molecular Ecology. 2006, 15 (4): 1109-1123. 10.1111\u002Fj.1365-294X.2006.02859.x.\nDuvernell DD, Lindmeier JB, Faust KE, Whitehead A: Relative influences of historical and contemporary forces shaping the distribution of genetic variation in the Atlantic killifish, Fundulus heteroclitus. Molecular Ecology. 2008, 17 (5): 1344-1360. 10.1111\u002Fj.1365-294X.2007.03648.x.\nWhitehead A, Crawford DL: Neutral and adaptive variation in gene expression. P Natl Acad Sci USA. 2006, 103 (14): 5425-5430. 10.1073\u002Fpnas.0507648103.\nGriffith RW: Environment and salinity tolerance in the genus Fundulus. Copeia. 1974, 319-331. 10.2307\u002F1442526.\nKidder GW, Petersen CW, Preston RL: Energetics of osmoregulation: I. Oxygen consumption by Fundulus heteroclitus. J Exp Zool Part A. 2006, 305A (4): 309-317. 10.1002\u002Fjez.a.251.\nKidder GW, Petersen CW, Preston RL: Energetics of osmoregulation: II. Water flux and osmoregulatory work in the euryhaline fish, Fundulus heteroclitus. J Exp Zool Part A. 2006, 305A (4): 318-327. 10.1002\u002Fjez.a.252.\nEvans DH, Piermarini PM, Choe KP: The multifunctional fish gill: Dominant site of gas exchange, osmoregulation, acid-base regulation, and excretion of nitrogenous waste. Physiological Reviews. 2005, 85 (1): 97-177. 10.1152\u002Fphysrev.00050.2003.\nChavez CH, Turgeon J: Asexual and sexual hybrids between Fundulus diaphanus and F. heteroclitus in the Canadian Atlantic region. Molecular Ecology. 2007, 16 (7): 1467-1480. 10.1111\u002Fj.1365-294X.2007.03239.x.\nDawley RM: Clonal hybrids of the common laboratory fish Fundulus heteroclitus. P Natl Acad Sci USA. 1992, 89 (6): 2485-2488. 10.1073\u002Fpnas.89.6.2485.\nLee JS, Miya M, Lee YS, Kim CG, Park EH, Aoki Y, Nishida M: The complete DNA sequence of the mitochondrial genome of the self fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish. Gene. 2001, 280 (1–2): 1-7. 10.1016\u002FS0378-1119(01)00765-X.\nMiya M, Nishida M: Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): First example of transfer RNA gene rearrangements in bony fishes. Mar Biotechnol. 1999, 1 (5): 416-426. 10.1007\u002FPL00011798.\nBonfield JK, Smith KF, Staden R: A new DNA sequence assembly program. Nucleic Acids Res. 1995, 23 (24): 4992-4999. 10.1093\u002Fnar\u002F23.24.4992.\nKumar S, Nei M, Dudley J, Tamura K: MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008, 9 (4): 299-306. 10.1093\u002Fbib\u002Fbbn017.\nLowe TM, Eddy SR: tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25 (5): 955-964. 10.1093\u002Fnar\u002F25.5.955.\nBernsel A, Viklund H, Falk J, Lindahl E, von Heijne G, Elofsson A: Prediction of membrane-protein topology from first principles. P Natl Acad Sci USA. 2008, 105 (20): 7177-7181. 10.1073\u002Fpnas.0711151105.\nGranseth E, Viklund H, Elofsson A: ZPRED: Predicting the distance to the membrane center for residues in alpha-helical membrane proteins. Bioinformatics. 2006, 22 (14): E191-E196. 10.1093\u002Fbioinformatics\u002Fbtl206.\nHessa T, Meindl-Beinker NM, Bernsel A, Kim H, Sato Y, Lerch-Bader M, Nilsson I, White SH, von Heijne G: Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature. 2007, 450 (7172): 1026-U1022. 10.1038\u002Fnature06387.\nViklund H, Elofsson A: Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Science. 2004, 13 (7): 1908-1917. 10.1110\u002Fps.04625404.\nViklund H, Elofsson A: OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics. 2008, 24 (15): 1662-1668. 10.1093\u002Fbioinformatics\u002Fbtn221.\nWoolley S, Johnson J, Smith MJ, Crandall KA, McClellan DA: TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees. Bioinformatics. 2003, 19 (5): 671-672. 10.1093\u002Fbioinformatics\u002Fbtg043.\nZhang JZ, Nielsen R, Yang ZH: Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 2005, 22 (12): 2472-2479. 10.1093\u002Fmolbev\u002Fmsi237.\nYang ZH: PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007, 24 (8): 1586-1591. 10.1093\u002Fmolbev\u002Fmsm088.\nMcdonald JH, Kreitman M: Adaptive Protein Evolution at the Adh Locus in Drosophila. Nature. 1991, 351 (6328): 652-654. 10.1038\u002F351652a0.\nRand DM, Kann LM: Mutation and selection at silent and replacement sites in the evolution of animal mitochondrial DNA. Genetica. 1998, 103: 393-407. 10.1023\u002FA:1017006118852.\nRand DM, Kann LM: Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol Biol Evol. 1996, 13 (6): 735-748.\nRozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R: DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 2003, 19 (18): 2496-2497. 10.1093\u002Fbioinformatics\u002Fbtg359.\nNachman MW: Deleterious mutations in animal mitochondrial DNA. Genetica. 1998, 103: 61-69. 10.1023\u002FA:1017030708374.\nRonquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19 (12): 1572-1574. 10.1093\u002Fbioinformatics\u002Fbtg180.\nClary DO, Wolstenholme DR: The mitochondrial DNA molecule of Drosophila yakuba – nucleotide sequence, gene organization, and genetic code. J Mol Evol. 1985, 22 (3): 252-271. 10.1007\u002FBF02099755.\nGaresse R: Drosophila melanogaster mitochondrial DNA: gene organization and evolutionary considerations. Genetics. 1988, 118 (4): 649-663.\nBrandt U: Energy converting NADH: Quinone oxidoreductase (Complex I). Annu Rev Biochem. 2006, 75: 69-92. 10.1146\u002Fannurev.biochem.75.103004.142539.\nda Fonseca RR, Johnson WE, O'Brien SJ, Ramos MJ, Antunes A: The adaptive evolution of the mammalian mitochondrial genome. Bmc Genomics. 2008, 9:\nHadikusumo RG, Meltzer S, Choo WM, Jeanfrancois MJB, Linnane AW, Marzuki S: The Definition of Mitochondrial H+-Atpase Assembly Defects in Mit-Mutants of Saccharomyces-Cerevisiae with a Monoclonal-Antibody to the Enzyme Complex as an Assembly Probe. Biochim Biophys Acta. 1988, 933 (1): 212-222. 10.1016\u002F0005-2728(88)90072-2.\nAnisimova M, Bielawski JP, Yang Z: Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol Biol Evol. 2002, 19 (6): 950-958.\nStewart JB, Freyer C, Elson JL, Wredenberg A, Cansu Z, Trifunovic A, Larsson N-G: Strong purifying selection in transmission of mammalian mitochondrial DNA. PLoS Biology. 2008, 6 (1): e10-10.1371\u002Fjournal.pbio.0060010.\nWeinreich DM, Rand DM: Contrasting Patterns of Nonneutral Evolution in Proteins Encoded in Nuclear and Mitochondrial Genomes. Genetics. 2000, 156 (1): 385-399.\nLee WJ, Conroy J, Howell WH, Kocher TD: Structure and evolution of teleost mitochondrial control regions. J Mol Evol. 1995, 41 (1): 54-66. 10.1007\u002FBF00174041.\nOhta T: Population size and rate of evolution. J Mol Evol. 1972, 1 (4): 305-314. 10.1007\u002FBF01653959.\nOhta T: Slightly deleterious mutant substitutions in evolution. Nature. 1973, 246 (5428): 96-98. 10.1038\u002F246096a0.\nBallard JWO: Comparative genomics of mitochondrial DNA in members of the Drosophila melanogaster subgroup. J Mol Evol. 2000, 51 (1): 48-63.\nWillett CS, Burton RS: Evolution of interacting proteins in the mitochondrial electron transport system in a marine copepod. Mol Biol Evol. 2004, 21 (3): 443-453. 10.1093\u002Fmolbev\u002Fmsh031.\nElson JL, Turnbull DM, Howell N: Comparative genomics and the evolution of human mitochondrial DNA: Assessing the effects of selection. Am J Hum Genet. 2004, 74 (2): 229-238. 10.1086\u002F381505.\nMiya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, et al: Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol. 2003, 26 (1): 121-138. 10.1016\u002FS1055-7903(02)00332-9.\nPhilpott CW, Copeland DE: Fine structure of chloride cells from three species of Fundulus. J Cell Biol. 1963, 18 (2): 389-404. 10.1083\u002Fjcb.18.2.389.\nRand DM, Haney RA, Fry AJ: Cytonuclear coevolution: the genomics of cooperation. Trends Ecol Evol. 2004, 19 (12): 645-653. 10.1016\u002Fj.tree.2004.10.003.",{"VOID":659},"10.1186\u002F1471-2148-9-11","2024-06-25T02:05:06.611+00:00","http:\u002F\u002Fbmcevolbiol.biomedcentral.com\u002Farticles\u002F10.1186\u002F1471-2148-9-11",[663],{"id":664,"sortIndex":19,"researcher":18,"roles":665,"affiliations":666,"properties":675},"3db5da88-5993-4acf-b702-df2ea14ab69c",[136],[667],{"id":668,"sortIndex":19,"affiliation":669,"properties":18},"41fa8c5c-779b-4f2b-a7c8-9a18e3eaca88",{"id":668,"createTime":18,"updateTime":18,"relativeEntities":670,"slug":18,"properties":671,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":674,"statistic":18},[],{"title":672},{"VI":673},"Department of Biological Sciences, Louisiana State University, Baton Rouge, USA",[],{"title":676,"gsAuthor":678},{"VI":677},"Andrew Whitehead",{"VOID":679},"[\"S9C9C8QAAAAJ\"]",{"url":661,"publisher":681,"properties":700},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":682,"slug":10,"properties":683,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":686,"manageAffiliations":687,"indexDatabases":688,"url":18,"thumbnailPath":18,"statistic":695,"gsStatistic":18,"type":18,"analyzePriority":18},[],{"title":684,"eissn":685},{"EN":13},{"VOID":15},[],[],[689],{"id":24,"indexDatabase":690,"url":35,"indexYears":36,"academicFieldIds":18,"indexDatabaseRanking":37},{"id":26,"createTime":18,"updateTime":18,"relativeEntities":691,"label":692,"description":693,"key":32,"publicationTags":694,"standard":18},[],{"EN":29,"VI":29},{"EN":29,"VI":31},[34],{"impactFactor":19,"impactFactorByYear":696,"i10Index":51,"i10IndexLast5Year":52,"totalPublication":53,"totalPublicationByYear":697,"totalCitation":70,"totalCitationByYear":698,"totalCitationPerPublication":88,"totalCitationPerPublicationByYear":699,"hindexLast5Year":105,"hindex":105},{"2012":40,"2013":41,"2014":42,"2015":43,"2016":44,"2017":45,"2018":46,"2019":47,"2020":48,"2021":49,"2022":50},{"2005":55,"2006":56,"2007":57,"2008":58,"2009":59,"2010":60,"2011":61,"2012":62,"2013":63,"2014":64,"2015":65,"2016":66,"2017":67,"2018":68,"2019":69,"2020":62},{"2005":72,"2006":73,"2007":74,"2008":75,"2009":76,"2010":77,"2011":78,"2012":79,"2013":80,"2014":81,"2015":82,"2016":83,"2017":84,"2018":85,"2019":86,"2020":87},{"2005":90,"2006":91,"2007":92,"2008":93,"2009":94,"2010":95,"2011":96,"2012":97,"2013":98,"2014":52,"2015":99,"2016":100,"2017":101,"2018":102,"2019":103,"2020":104},{"pages":701,"volume":703},{"VOID":702},"1-13",{"VOID":704},"9",{"total":19,"publishYear":706,"statisticByYear":707},2009,{},"2009-01-13","DONE_ANALYZE_CITATION",[37],{"id":712,"createTime":713,"updateTime":714,"relativeEntities":715,"slug":716,"properties":717,"entityType":127,"verifyStatus":128,"verifyTime":728,"verifyNote":130,"languages":18,"translateLanguages":18,"viewCount":19,"primaryUrl":729,"fullTextUrl":18,"authors":730,"publicationType":241,"publisherRelationship":748,"citationCount":19,"citationInfo":772,"publishDate":774,"publishYear":706,"citationAnalyzeStatus":709,"lastCitationAnalyze":775,"indexDatabases":776,"openAccess":18,"references":18,"isForceReanalyzing":274},"922f29ed-0423-492c-8141-23164dbf5e8a","2024-01-13T10:19:48.036+00:00","2026-07-28T17:54:57.080+00:00",[],"Intronization-de-intronization-and-intron-sliding-are-rare-in-Cryptococcus",{"abstract":718,"title":720,"gsPaper":722,"references":724,"doi":726},{"EN":719},"Eukaryotic pre-mRNA gene transcripts are processed by the spliceosome to remove portions of the transcript, called spliceosomal introns. The spliceosome recognizes intron boundaries by the presence of sequence signals (motifs) contained in the actual transcript, thus sequence changes in the genome that affect existing splicing signals or create new signals may lead to changes in transcript splicing patterns. Such changes may lead to previously excluded (intronic) transcript regions being included (exonic) or vice versa. Such changes can affect the encoded protein sequence and\u002For post-transcriptional regulation, and are thus a potentially important source of genomic and phenotypic novelty. Two recent papers suggest that such changes may be a major force in remodeling of eukaryotic gene structures, however the rate of occurrence of such changes has not been assessed at the genomic level. I studied four closely related species of Cryptoccocus fungi. Among 28,256 studied introns, canonical GT\u002FC...AG boundaries are nearly universally conserved across all four species. Among only 40 observed cases of cDNA-confirmed non-conserved intron boundaries, most are likely to involve alternative splicing. I find only five cases of \"intronization,\" intron creation from an internal exonic region by de novo emergence of new splicing boundaries, and no cases of the reverse process, \"de-intronization.\" I find no more than ten clear cases of true movement of an intron boundary of a possibly constitutively spliced intron, and no clear cases of true \"intron sliding,\" in which changes in the positions of both intron boundaries could lead to a movement of the intron position along the coding sequence. These results suggest that intronization, de-intronization, and intron boundary movement are rare events in evolution.",{"EN":721},"Intronization, de-intronization and intron sliding are rare in Cryptococcus",{"VOID":723},"[\"9025804269964463831\"]",{"VOID":725},"Mironov AA, Fickett JW, Gelfand MS: Frequent alternative splicing of human genes. Genome Res. 1999, 9 (12): 1288-93. 10.1101\u002Fgr.9.12.1288.\nFedorov A, Merican AF, Gilbert W: Large-scale comparison of intron positions among animal, plant, and fungal genomes. Proc Natl Acad Sci USA. 2002, 99 (25): 16128-16133. 10.1073\u002Fpnas.242624899.\nPerler F, Efstratiadis A, Lomedico P, Gilbert W, Kolodner R, Dodgson J: The evolution of genes: the chicken preproinsulin gene. Cell. 1980, 20 (2): 555-66. 10.1016\u002F0092-8674(80)90641-8.\nRogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV: Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol. 2003, 13 (17): 1512-7. 10.1016\u002FS0960-9822(03)00558-X.\nRoy SW, Fedorov A, Gilbert W: Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain. Proc Natl Acad Sci USA. 2003, 100 (12): 7158-62. 10.1073\u002Fpnas.1232297100.\nCarmel L, Wolf YI, Rogozin IB, Koonin EV: Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res. 2007, 17 (7): 1034-44. 10.1101\u002Fgr.6438607.\nCsurös M, Rogozin IB, Koonin EV: Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach. Mol Biol Evol. 2008, 25 (5): 903-11. 10.1093\u002Fmolbev\u002Fmsn039.\nOmilian AR, Scofiend DG, Lynch M: Intron presence-absence polymorphism in Daphnia. Mol Biol Evol. 2008, 25 (10): 2129-2139. 10.1093\u002Fmolbev\u002Fmsn164.\nIrimia M, Rukov JL, Penny D, Vinther J, Garcia-Fernandez J, Roy SW: Origin of introns by 'intronization' of exonic sequences. Trends Genet. 2008, 24 (8): 378-81. 10.1016\u002Fj.tig.2008.05.007.\nLev-Maor G, Sorek R, Shomron N, Ast G: The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science. 2003, 300 (5623): 1288-91. 10.1126\u002Fscience.1082588.\nLlopart A, Comeron JM, Brunet FG, Lachaise D, Long M: Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection. Proc Natl Acad Sci USA. 2002, 99 (12): 8121-6. 10.1073\u002Fpnas.122570299.\nModrek B, Lee C: A genomic view of alternative splicing. Nat Genet. 2002, 30 (1): 13-19. 10.1038\u002Fng0102-13.\nCrick F: Split genes and RNA splicing. Science. 1979, 204: 264-271. 10.1126\u002Fscience.373120.\nRoy SW: The origin of recent introns: transposons?. Genome Biol. 2004, 5 (12): 251-10.1186\u002Fgb-2004-5-12-251.\nBell GI, Sanchez-Pescador R, Laybourn PJ, Najarian RC: Exon duplication and divergence in the human preproglucagon gene. Nature. 1983, 304 (5924): 368-371. 10.1038\u002F304368a0.\nFedorov A, Fedorova L, Starshenko V, Filatov V, Grigor'ev E: Influence of exon duplication on intron and exon phase distribution. J Mol Evol. 1998, 46 (3): 263-271. 10.1007\u002FPL00006302.\nRogers JH: How were introns inserted into nuclear genes?. Trends Genet. 1989, 5 (7): 213-6. 10.1016\u002F0168-9525(89)90084-X.\nFairbrother WG, Yah RF, Sharp PA, Burge CB: Predictive identification of exonic splicing enhancers in human genes. Science. 2002, 297: 1007-13. 10.1126\u002Fscience.1073774.\nKoren E, Lev-Maor G, Ast G: The emergence of alternative 3' and 5' splice site exons from constitutive exons. PLoS Comput Biol. 2007, 3 (5): e95-10.1371\u002Fjournal.pcbi.0030095.\nLonberg E, Gilbert W: Intron\u002Fexon structure of the chicken pyruvate kinase gene. Cell. 1985, 40 (1): 81-90. 10.1016\u002F0092-8674(85)90311-3.\nLu ZX, Peng J, Su B: A human-specific mutation leads to the origin of a novel splice form of neuropsin (KLK8), a gene involved in learning and memory. Hum Mutat. 2007, 28 (10): 978-84. 10.1002\u002Fhumu.20547.\nTarrío R, Ayala FJ, Rodríguez-Trelles F: Alternative splicing: a missing piece in the puzzle of intron gain. Proc Natl Acad Sci USA. 2008, 105 (20): 7223-8. 10.1073\u002Fpnas.0802941105.\nCatania F, Lynch M: Where do introns come from?. PLoS Biol. 2008, 6: e283-10.1371\u002Fjournal.pbio.0060283.\nHughes SS, Buckley CO, Neafsey DE: Complex selection on intron size in Cryptococcus neoformans. Mol Biol Evol. 2008, 25 (2): 247-53. 10.1093\u002Fmolbev\u002Fmsm220.\nLoftus BJ, et al: The genome of the basidiomycetous yeast and human pathogen Cryptoccus neoformans. Science. 2005, 307: 1321-4. 10.1126\u002Fscience.1103773.\nMcGuire AM, Pearson MD, Neafsey DE, Galagan JE: Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol. 2008, 9: R50-10.1186\u002Fgb-2008-9-3-r50.\nStajich JE, Dietrich FS: Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans. Euk Cell. 2004, 5: 789-93. 10.1128\u002FEC.5.5.789-793.2006.\nSharpton TJ, Neafsey DE, Galagan JE, Taylor JW: Mechanisms of intron gain and loss in Cryptococcus. Genome Biol. 2008, 9 (1): R24-10.1186\u002Fgb-2008-9-1-r24.\nRoy SW, Penny D, Neafsey DE: Evolutionary conservation of UTR intron boundaries in Cryptococcus. Mol Biol Evol. 2007, 24 (5): 1140-8. 10.1093\u002Fmolbev\u002Fmsm045.\nRogozin IB, Lyons-Weiler J, Koonin EV: Intron sliding in conserved gene families. Trends Genet. 2000, 16 (10): 430-2. 10.1016\u002FS0168-9525(00)02096-5.\nSakharkar MK, Tan TW, de Souza SJ: Generation of a database containing discordant intron positions in eukaryotic genes (MIDB). Bioinformatics. 2001, 17 (8): 671-5. 10.1093\u002Fbioinformatics\u002F17.8.671.\nIrimia M, Penny D, Roy SW: Coevolution of genomic intron number and splice sites. Trends Genet. 2007, 23 (7): 321-5. 10.1016\u002Fj.tig.2007.04.001.\nIrimia M, Roy SW: Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome. PLoS Genet. 2008, 4: e1000148-10.1371\u002Fjournal.pgen.1000148.\nLynch M, Conery JS: The origins of genome complexity. Science. 2003, 302: 1401-1404. 10.1126\u002Fscience.1089370.\nLynch M: The origins of eukaryotic gene structure. Mol Biol Evol. 2006, 23: 450-68. 10.1093\u002Fmolbev\u002Fmsj050.\nMakalowski W, Boguski MS: Evolutionary parameters of the transcribed mammalian genome: an analysis of. Proc Natl Acad Sci USA. 1998, 95: 9407-9412. 10.1073\u002Fpnas.95.16.9407.\nWaterson RH, et al: Initial sequencing and comparative analysis of the mouse genome. Nature. 2002, 420: 520-562. 10.1038\u002Fnature01262.\nTamura K, Subramanian S, Kumar S: Temporal patterns of fruit fly evolution revealed by molecular clocks. Mol Biol Evol. 2004, 21: 36-44. 10.1093\u002Fmolbev\u002Fmsg236.\nNeafsey DE, Hartl DL, Berriman M: Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes. Mol Biol Evol. 2005, 22: 1621-1626. 10.1093\u002Fmolbev\u002Fmsi154.\nKasuga T, White TJ, Taylor JW: Estimation of nucleotide substitution rates in Eurotiomycete fungi. Mol Biol Evol. 2002, 19: 2318-2324.\nCsuros M: Likely scenarios of intron evolution. LNCS. 2005, 3678: 47-60.\nRoy SW, Gilbert W: Rates of intron loss and gain: implications for early eukaryotic evolution. Proc Natl Acad Sci USA. 2005, 102: 5773-8. 10.1073\u002Fpnas.0500383102.\nStajich JE, Dietrich FS, Roy SW: Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biol. 2007, 8: R223-10.1186\u002Fgb-2007-8-10-r223.",{"VOID":727},"10.1186\u002F1471-2148-9-192","2024-06-26T23:07:12.320+00:00","https:\u002F\u002Fbmcecolevol.biomedcentral.com\u002Farticles\u002F10.1186\u002F1471-2148-9-192",[731],{"id":732,"sortIndex":19,"researcher":18,"roles":733,"affiliations":734,"properties":743},"47ef3dda-ad42-4815-b7e9-f75fd7b77ec4",[136],[735],{"id":736,"sortIndex":19,"affiliation":737,"properties":18},"13c7858e-8190-4640-b082-e53ed7e02fd8",{"id":736,"createTime":18,"updateTime":18,"relativeEntities":738,"slug":18,"properties":739,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":742,"statistic":18},[],{"title":740},{"VI":741},"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA.",[],{"title":744,"gsAuthor":746},{"VI":745},"Scott W Roy",{"VOID":747},"[\"rJuPCHcAAAAJ\"]",{"url":729,"publisher":749,"properties":768},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":750,"slug":10,"properties":751,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":754,"manageAffiliations":755,"indexDatabases":756,"url":18,"thumbnailPath":18,"statistic":763,"gsStatistic":18,"type":18,"analyzePriority":18},[],{"title":752,"eissn":753},{"EN":13},{"VOID":15},[],[],[757],{"id":24,"indexDatabase":758,"url":35,"indexYears":36,"academicFieldIds":18,"indexDatabaseRanking":37},{"id":26,"createTime":18,"updateTime":18,"relativeEntities":759,"label":760,"description":761,"key":32,"publicationTags":762,"standard":18},[],{"EN":29,"VI":29},{"EN":29,"VI":31},[34],{"impactFactor":19,"impactFactorByYear":764,"i10Index":51,"i10IndexLast5Year":52,"totalPublication":53,"totalPublicationByYear":765,"totalCitation":70,"totalCitationByYear":766,"totalCitationPerPublication":88,"totalCitationPerPublicationByYear":767,"hindexLast5Year":105,"hindex":105},{"2012":40,"2013":41,"2014":42,"2015":43,"2016":44,"2017":45,"2018":46,"2019":47,"2020":48,"2021":49,"2022":50},{"2005":55,"2006":56,"2007":57,"2008":58,"2009":59,"2010":60,"2011":61,"2012":62,"2013":63,"2014":64,"2015":65,"2016":66,"2017":67,"2018":68,"2019":69,"2020":62},{"2005":72,"2006":73,"2007":74,"2008":75,"2009":76,"2010":77,"2011":78,"2012":79,"2013":80,"2014":81,"2015":82,"2016":83,"2017":84,"2018":85,"2019":86,"2020":87},{"2005":90,"2006":91,"2007":92,"2008":93,"2009":94,"2010":95,"2011":96,"2012":97,"2013":98,"2014":52,"2015":99,"2016":100,"2017":101,"2018":102,"2019":103,"2020":104},{"pages":769,"volume":771},{"VOID":770},"1-10",{"VOID":704},{"total":19,"publishYear":706,"statisticByYear":773},{},"2009-08-07","2026-07-28T17:54:57.079+00:00",[37],{"id":778,"createTime":779,"updateTime":780,"relativeEntities":781,"slug":782,"properties":783,"entityType":127,"verifyStatus":128,"verifyTime":792,"verifyNote":130,"languages":18,"translateLanguages":18,"viewCount":19,"primaryUrl":793,"fullTextUrl":18,"authors":794,"publicationType":241,"publisherRelationship":864,"citationCount":889,"citationInfo":890,"publishDate":893,"publishYear":891,"citationAnalyzeStatus":271,"lastCitationAnalyze":894,"indexDatabases":895,"openAccess":18,"references":896,"isForceReanalyzing":274},"9347da8a-4180-48d7-8068-f68456f46ba2","2024-01-17T15:58:03.049+00:00","2026-07-28T01:40:50.180+00:00",[],"Evolutionary-origin-of-type-IV-classical-cadherins-in-arthropods",{"abstract":784,"title":786,"gsPaper":788,"doi":790},{"EN":785},"Classical cadherins are a metazoan-specific family of homophilic cell-cell adhesion molecules that regulate morphogenesis. Type I and type IV cadherins in this family function at adherens junctions in the major epithelial tissues of vertebrates and insects, respectively, but they have distinct, relatively simple domain organizations that are thought to have evolved by independent reductive changes from an ancestral type III cadherin, which is larger than derived paralogs and has a complicated domain organization. Although both type III and type IV cadherins have been identified in hexapods and branchiopods, the process by which the type IV cadherin evolved is still largely unclear. Through an analysis of arthropod genome sequences, we found that the only classical cadherin encoded in chelicerate genomes was the type III cadherin and that the two type III cadherin genes found in the spider Parasteatoda tepidariorum genome exhibited a complex yet ancestral exon-intron organization in arthropods. Genomic and transcriptomic data from branchiopod, copepod, isopod, amphipod, and decapod crustaceans led us to redefine the type IV cadherin category, which we separated into type IVa and type IVb, which displayed a similar domain organization, except type IVb cadherins have a larger number of extracellular cadherin (EC) domains than do type IVa cadherins (nine versus seven). We also showed that type IVa cadherin genes occurred in the hexapod, branchiopod, and copepod genomes whereas only type IVb cadherin genes were present in malacostracans. Furthermore, comparative characterization of the type IVb cadherins suggested that the presence of two extra EC domains in their N-terminal regions represented primitive characteristics. In addition, we identified an evolutionary loss of two highly conserved cysteine residues among the type IVa cadherins of insects. We provide a genomic perspective of the evolution of classical cadherins among bilaterians, with a focus on the Arthropoda, and suggest that following the divergence of early arthropods, the precursor of the insect type IV cadherin evolved through stepwise reductive changes from the ancestral type III state. In addition, the complementary distributions of polarized genomic characters related to type IVa\u002FIVb cadherins may have implications for our interpretations of pancrustacean phylogeny.",{"EN":787},"Evolutionary origin of type IV classical cadherins in arthropods",{"VOID":789},"[\"15604928146991422046\"]",{"VOID":791},"10.1186\u002Fs12862-017-0991-2","2024-05-04T17:31:50.937+00:00","https:\u002F\u002Fbmcecolevol.biomedcentral.com\u002Farticles\u002F10.1186\u002Fs12862-017-0991-2",[795,819,841],{"id":796,"sortIndex":19,"researcher":18,"roles":797,"affiliations":798,"properties":816},"7aa09532-77f5-46cf-a54e-620aabdb60b6",[136],[799,807],{"id":800,"sortIndex":19,"affiliation":801,"properties":18},"31c974cd-9a4f-4ea2-a177-db6b329067e6",{"id":800,"createTime":18,"updateTime":18,"relativeEntities":802,"slug":18,"properties":803,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":806,"statistic":18},[],{"title":804},{"VI":805},"Laboratory of Evolutionary Cell and Developmental Biology, JT Biohistory Research Hall, Takatsuki, Japan",[],{"id":808,"sortIndex":148,"affiliation":809,"properties":815},"d6ef0d81-564a-4983-93d2-3a18839f4999",{"id":808,"createTime":18,"updateTime":18,"relativeEntities":810,"slug":18,"properties":811,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":814,"statistic":18},[],{"title":812},{"VI":813},"Current address: Department of Parasitology, Asahikawa Medical University, Asahikawa, Japan",[],{},{"title":817},{"VI":818},"Mizuki Sasaki",{"id":820,"sortIndex":148,"researcher":18,"roles":821,"affiliations":822,"properties":838},"88e8860b-4061-46ad-8c64-b8df66a5f218",[136],[823,829],{"id":800,"sortIndex":19,"affiliation":824,"properties":18},{"id":800,"createTime":18,"updateTime":18,"relativeEntities":825,"slug":18,"properties":826,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":828,"statistic":18},[],{"title":827},{"VI":805},[],{"id":830,"sortIndex":148,"affiliation":831,"properties":837},"3fbe8a0f-a457-4c9b-bdc1-e1b39d11ca4d",{"id":830,"createTime":18,"updateTime":18,"relativeEntities":832,"slug":18,"properties":833,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":836,"statistic":18},[],{"title":834},{"VI":835},"Department of Microbiology and Infection Control, Osaka Medical College, Takatsuki, Japan",[],{},{"title":839},{"VI":840},"Yasuko Akiyama-Oda",{"id":842,"sortIndex":179,"researcher":18,"roles":843,"affiliations":844,"properties":859},"3f1f7aa5-4d17-4a40-90de-caaeac5e8a7a",[136],[845,851],{"id":800,"sortIndex":19,"affiliation":846,"properties":18},{"id":800,"createTime":18,"updateTime":18,"relativeEntities":847,"slug":18,"properties":848,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":850,"statistic":18},[],{"title":849},{"VI":805},[],{"id":852,"sortIndex":148,"affiliation":853,"properties":18},"64be180e-cda7-47c2-a9f0-c145a33cf5ee",{"id":852,"createTime":18,"updateTime":18,"relativeEntities":854,"slug":18,"properties":855,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":858,"statistic":18},[],{"title":856},{"VI":857},"Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan",[],{"title":860,"gsAuthor":862},{"VI":861},"Hiroki Oda",{"VOID":863},"[\"sLDeAYcAAAAJ\"]",{"url":793,"publisher":865,"properties":884},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":866,"slug":10,"properties":867,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":870,"manageAffiliations":871,"indexDatabases":872,"url":18,"thumbnailPath":18,"statistic":879,"gsStatistic":18,"type":18,"analyzePriority":18},[],{"title":868,"eissn":869},{"EN":13},{"VOID":15},[],[],[873],{"id":24,"indexDatabase":874,"url":35,"indexYears":36,"academicFieldIds":18,"indexDatabaseRanking":37},{"id":26,"createTime":18,"updateTime":18,"relativeEntities":875,"label":876,"description":877,"key":32,"publicationTags":878,"standard":18},[],{"EN":29,"VI":29},{"EN":29,"VI":31},[34],{"impactFactor":19,"impactFactorByYear":880,"i10Index":51,"i10IndexLast5Year":52,"totalPublication":53,"totalPublicationByYear":881,"totalCitation":70,"totalCitationByYear":882,"totalCitationPerPublication":88,"totalCitationPerPublicationByYear":883,"hindexLast5Year":105,"hindex":105},{"2012":40,"2013":41,"2014":42,"2015":43,"2016":44,"2017":45,"2018":46,"2019":47,"2020":48,"2021":49,"2022":50},{"2005":55,"2006":56,"2007":57,"2008":58,"2009":59,"2010":60,"2011":61,"2012":62,"2013":63,"2014":64,"2015":65,"2016":66,"2017":67,"2018":68,"2019":69,"2020":62},{"2005":72,"2006":73,"2007":74,"2008":75,"2009":76,"2010":77,"2011":78,"2012":79,"2013":80,"2014":81,"2015":82,"2016":83,"2017":84,"2018":85,"2019":86,"2020":87},{"2005":90,"2006":91,"2007":92,"2008":93,"2009":94,"2010":95,"2011":96,"2012":97,"2013":98,"2014":52,"2015":99,"2016":100,"2017":101,"2018":102,"2019":103,"2020":104},{"pages":885,"volume":887},{"VOID":886},"1-23",{"VOID":888},"17",21,{"total":889,"publishYear":891,"statisticByYear":892},2017,{"2018":179,"2019":179,"2020":179,"2021":50,"2022":56,"2023":148,"2024":179,"2025":148},"2017-06-17","2026-07-28T01:40:50.179+00:00",[37],[897,903,906,909,912,915,918,921,924,927,930,933,936,939,942,945,951,954,957,960,963,966,969,972,975,978,981,984,987,990,993,996,999,1002,1005,1011,1014,1017,1020,1023,1026,1029,1032,1035,1038,1041,1044,1050,1053,1056,1059,1062,1065,1068,1074,1077,1080,1083,1086,1089,1092,1095,1098,1101,1104,1110,1116,1122,1125,1128,1131,1134,1137,1140,1143,1146,1149,1152,1155,1161,1164,1170,1173,1176,1179,1186],{"id":898,"text":899,"url":900,"identifiers":901},"4c68646b-0035-4279-8000-0006b275d4fa","Hulpiau P, van Roy F. Molecular evolution of the cadherin superfamily. Int J Biochem Cell Biol. 2009;41:349–69.","https:\u002F\u002Flink.springer.com\u002F10.1007\u002Fs10440-022-00541-7",{"doi":902},"10.1007\u002Fs10440-022-00541-7",{"id":898,"text":904,"url":900,"identifiers":905},"Hulpiau P, Van Roy F. New insights into the evolution of metazoan Cadherins. Mol Biol Evol. 2010;28:647–57.",{"doi":902},{"id":898,"text":907,"url":900,"identifiers":908},"Oda H, Takeichi M. Evolution: structural and functional diversity of cadherin at the adherens junction. J Cell Biol. 2011;193:1137–46.",{"doi":902},{"id":898,"text":910,"url":900,"identifiers":911},"Gumbiner BM. Regulation of cadherin-mediated adhesion in morphogenesis. Nat Rev Mol Cell Biol. 2005;6:622–34.",{"doi":902},{"id":898,"text":913,"url":900,"identifiers":914},"Harris TJC, Tepass U. Adherens junctions: from molecules to morphogenesis. Nat Rev Mol Cell Biol. 2010;11:502–14.",{"doi":902},{"id":898,"text":916,"url":900,"identifiers":917},"Guillot C, Lecuit T. Mechanics of epithelial tissue homeostasis and morphogenesis. Science. 2013;340:1185–9.",{"doi":902},{"id":898,"text":919,"url":900,"identifiers":920},"Takeichi M. Dynamic contacts: rearranging adherens junctions to drive epithelial remodelling. Nat Rev Mol Cell Biol. 2014;15:397–410.",{"doi":902},{"id":898,"text":922,"url":900,"identifiers":923},"Nose A, Tsuji K, Takeichi M. Localization of specificity determining sites in cadherin cell adhesion molecules. Cell. 1990;61:147–55.",{"doi":902},{"id":898,"text":925,"url":900,"identifiers":926},"Vendome J, Felsovalyi K, Song H, Yang Z, Jin X, Brasch J, et al. Structural and energetic determinants of adhesive binding specificity in type I cadherins. Proc Natl Acad Sci U S A. 2014;111:E4175–84.",{"doi":902},{"id":898,"text":928,"url":900,"identifiers":929},"Ozawa M, Ringwald M, Kemler R. Uvomorulin-catenin complex formation is regulated by a specific domain in the cytoplasmic region of the cell adhesion molecule. Proc Natl Acad Sci U S A. 1990;87:4246–50.",{"doi":902},{"id":898,"text":931,"url":900,"identifiers":932},"Mammoto T, Ingber DE. Mechanical control of tissue and organ development. Development. 2010;137:1407–20.",{"doi":902},{"id":898,"text":934,"url":900,"identifiers":935},"Lecuit T, Yap AS. E-cadherin junctions as active mechanical integrators in tissue dynamics. Nat Cell Biol. 2015;17:533–9.",{"doi":902},{"id":898,"text":937,"url":900,"identifiers":938},"Heisenberg CP, Bellaïche Y. Forces in tissue morphogenesis and patterning. Cell. 2013;153:948–62.",{"doi":902},{"id":18,"text":940,"url":18,"identifiers":941},"Sasakura Y, Shoguchi E, Takatori N, Wada S, Meinertzhagen IA, Satou Y, et al. A genomewide survey of developmentally relevant genes in Ciona intestinalis. X. Genes for cell junctions and extracellular matrix. Dev Genes Evol. 2003;213:303–13.",{},{"id":898,"text":943,"url":900,"identifiers":944},"Oda H, Tagawa K, Akiyama-Oda Y. Diversification of epithelial adherens junctions with independent reductive changes in cadherin form: identification of potential molecular synapomorphies among bilaterians. Evol Dev. 2005;7:376–89.",{"doi":902},{"id":946,"text":947,"url":948,"identifiers":949},"6566b39e-4f56-405b-98cd-5153e5da582a","Whittaker CA, Bergeron K-FF, Whittle J, Brandhorst BP, Burke RD, Hynes RO. The echinoderm adhesome. Dev Biol. 2006;300:252–66.","https:\u002F\u002Fwww.sciencedirect.com\u002Fscience\u002Farticle\u002Fpii\u002FS001216060601058X",{"doi":950},"10.1016\u002Fj.ydbio.2006.07.044",{"id":898,"text":952,"url":900,"identifiers":953},"Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, et al. The dynamic genome of Hydra. Nature. 2010;464:592–6.",{"doi":902},{"id":898,"text":955,"url":900,"identifiers":956},"Fahey B, Degnan BM. Origin of animal epithelia: insights from the sponge genome. Evol Dev. 2010;12:601–17.",{"doi":902},{"id":898,"text":958,"url":900,"identifiers":959},"Nichols SA, Roberts BW, Richter DJ, Fairclough SR, King N. Origin of metazoan cadherin diversity and the antiquity of the classical cadherin\u002Fβ-catenin complex. Proc Natl Acad Sci U S A. 2012;109:13046–51.",{"doi":902},{"id":898,"text":961,"url":900,"identifiers":962},"Tanabe K, Takeichi M, Nakagawa S. Identification of a nonchordate-type classic cadherin in vertebrates: chicken Hz-cadherin is expressed in horizontal cells of the neural retina and contains a nonchordate-specific domain complex. Dev Dyn. 2004;229:899–906.",{"doi":902},{"id":898,"text":964,"url":900,"identifiers":965},"Levi L, Douek J, Osman M, Bosch TC, Rinkevich B. Cloning and characterization of BS-cadherin, a novel cadherin from the colonial urochordate Botryllus schlosseri. Gene. 1997;200:117–23.",{"doi":902},{"id":898,"text":967,"url":900,"identifiers":968},"Oda H, Uemura T, Harada Y, Iwai Y, Takeichi M. A Drosophila homolog of cadherin associated with armadillo and essential for embryonic cell-cell adhesion. Dev Biol. 1994;165:716–26.",{"doi":902},{"id":898,"text":970,"url":900,"identifiers":971},"Uemura T, Oda H, Kraut R, Hayashi S, Kotaoka Y, Takeichi M. Zygotic Drosophila E-cadherin expression is required for processes of dynamic epithelial cell rearrangement in the drosophila embryo. Genes Dev. 1996;10:659–71.",{"doi":902},{"id":898,"text":973,"url":900,"identifiers":974},"Tepass U, Gruszynski-DeFeo E, Haag TA, Omatyar L, Török T, Hartenstein V. shotgun encodes Drosophila E-cadherin and is preferentially required during cell rearrangement in the neurectoderm and other morphogenetically active epithelia. Genes Dev. 1996;10:672–85.",{"doi":902},{"id":898,"text":976,"url":900,"identifiers":977},"Oda H, Tsukita S. Nonchordate classic cadherins have a structurally and functionally unique domain that is absent from chordate classic cadherins. Dev Biol. 1999;216:406–22.",{"doi":902},{"id":898,"text":979,"url":900,"identifiers":980},"Haruta T, Warrior R, Yonemura S, Oda H. The proximal half of the Drosophila E-cadherin extracellular region is dispensable for many cadherin-dependent events but required for ventral furrow formation. Genes Cells. 2010;15:193–208.",{"doi":902},{"id":898,"text":982,"url":900,"identifiers":983},"Nishiguchi S, Yagi A, Sakai N, Oda H. Divergence of structural strategies for homophilic E-cadherin binding among bilaterians. J Cell Sci. 2016;129:3309–19.",{"doi":902},{"id":898,"text":985,"url":900,"identifiers":986},"Iwai Y, Usui T, Hirano S, Steward R, Takeichi M, Uemura T. Axon patterning requires DN-cadherin, a novel neuronal adhesion receptor, in the Drosophila embryonic CNS. Neuron. 1997;19:77–89.",{"doi":902},{"id":898,"text":988,"url":900,"identifiers":989},"Miller JR, McClay DR. Characterization of the role of cadherin in regulating cell adhesion during sea urchin development. Dev Biol. 1997;192:323–39.",{"doi":902},{"id":898,"text":991,"url":900,"identifiers":992},"Takeichi M. The cadherin superfamily in neuronal connections and interactions. Nat Rev Neurosci. 2007;8:11–20.",{"doi":902},{"id":898,"text":994,"url":900,"identifiers":995},"Costa M, Raich W, Agbunag C, Leung B, Hardin J, Priess JR. A putative catenin-cadherin system mediates morphogenesis of the Caenorhabditis elegans embryo. J Cell Biol. 1998;141:297–308.",{"doi":902},{"id":898,"text":997,"url":900,"identifiers":998},"Oda H, Akiyama-Oda Y, Zhang S. Two classic cadherin-related molecules with no cadherin extracellular repeats in the cephalochordate amphioxus: distinct adhesive specificities and possible involvement in the development of multicell-layered structures. J Cell Sci. 2004;117:2757–67.",{"doi":902},{"id":898,"text":1000,"url":900,"identifiers":1001},"Oda H, Wada H, Tagawa K, Akiyama-Oda Y, Satoh N, Humphreys T, et al. A novel amphioxus cadherin that localizes to epithelial adherens junctions has an unusual domain organization with implications for chordate phylogeny. Evol Dev. 2002;4:426–34.",{"doi":902},{"id":898,"text":1003,"url":900,"identifiers":1004},"Oda H. Evolution of the cadherin-catenin complex. Subcell Biochem. 2012;60:9–35.",{"doi":902},{"id":1006,"text":1007,"url":1008,"identifiers":1009},"0e311a9a-ba78-4732-a84c-0924ae4acb2b","Sigrist CJ, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, et al. New and continuing developments at PROSITE. Nucleic Acids Res. 2013;41:D344–7.","http:\u002F\u002Facademic.oup.com\u002Fnar\u002Farticle\u002F41\u002FD1\u002FD344\u002F1055798\u002FNew-and-continuing-developments-at-PROSITE",{"doi":1010},"10.1093\u002Fnar\u002Fgks1067",{"id":18,"text":1012,"url":18,"identifiers":1013},"Jin X, Walker MA, Felsövályi K, Vendome J, Bahna F, Mannepalli S, et al. Crystal structures of Drosophila N-cadherin ectodomain regions reveal a widely used class of Ca2+-free interdomain linkers. Proc Natl Acad Sci USA. 2012;109:E127–34.",{},{"id":898,"text":1015,"url":900,"identifiers":1016},"i5K Consortium. The i5K initiative: advancing arthropod genomics for knowledge, human health, agriculture, and the environment. J Hered. 2013;104:595–600.",{"doi":902},{"id":898,"text":1018,"url":900,"identifiers":1019},"Sanggaard KW, Bechsgaard JS, Fang X, Duan J, Dyrlund TF, Gupta V, et al. Spider genomes provide insight into composition and evolution of venom and silk. Nat Commun. 2014;5:3765.",{"doi":902},{"id":898,"text":1021,"url":900,"identifiers":1022},"Grbić M, Van Leeuwen T, Clark RM, Rombauts S, Rouzé P, Grbić V, et al. The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature. 2011;479:487–92.",{"doi":902},{"id":898,"text":1024,"url":900,"identifiers":1025},"Hoy MA, Waterhouse RM, Wu K, Estep AS, Ioannidis P, Palmer WJ, et al. Genome sequencing of the phytoseiid predatory mite Metaseiulus occidentalis reveals completely atomized Hox genes and superdynamic intron evolution. Genome Biol Evol. 2016;8:1762–75.",{"doi":902},{"id":898,"text":1027,"url":900,"identifiers":1028},"Cao Z, Yu Y, Wu Y, Hao P, Di Z, He Y, et al. The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods. Nat Commun. 2013;4:2602.",{"doi":902},{"id":898,"text":1030,"url":900,"identifiers":1031},"Chipman AD, Ferrier DE, Brena C, Qu J, Hughes DS, Schröder R, et al. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima. PLoS Biol. 2014;12:e1002005.",{"doi":902},{"id":18,"text":1033,"url":18,"identifiers":1034},"Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, et al. The ecoresponsive genome of Daphnia pulex. Science. 2011;331:555–61.",{},{"id":898,"text":1036,"url":900,"identifiers":1037},"Kao D, Lai AG, Stamataki E, Rosic S, Konstantinides N, Jarvis E, et al. The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. elife. 2016;5",{"doi":902},{"id":898,"text":1039,"url":900,"identifiers":1040},"Greenwood MD, Marsden MD, Cowley CM, Sahota VK, Buxton RS. Exon-intron organization of the human type 2 desmocollin gene (DSC2): desmocollin gene structure is closer to “classical” cadherins than to desmogleins. Genomics. 1997;44:330–5.",{"doi":902},{"id":898,"text":1042,"url":900,"identifiers":1043},"Huber P, Dalmon J, Engiles J, Breviario F, Gory S, Siracusa LD, et al. Genomic structure and chromosomal mapping of the mouse VE-cadherin gene (Cdh5). Genomics. 1996;32:21–8.",{"doi":902},{"id":1045,"text":1046,"url":1047,"identifiers":1048},"e5294384-1cbb-455c-94c2-16862017851e","Jung R, Wendeler MW, Danevad M, Himmelbauer H, Gessner R. Phylogenetic origin of LI-cadherin revealed by protein and gene structure analysis. Cell Mol Life Sci. 2004;61:1157–66.","http:\u002F\u002Flink.springer.com\u002F10.1007\u002Fs00018-004-3470-z",{"doi":1049},"10.1007\u002Fs00018-004-3470-z",{"id":18,"text":1051,"url":18,"identifiers":1052},"Ozawa M, Hoschützky H, Herrenknecht K, Kemler R. A possible new adhesive site in the cell-adhesion molecule uvomorulin. Mech Dev. 1990;33:49–56.",{},{"id":898,"text":1054,"url":900,"identifiers":1055},"Chen X, Molino C, Liu L, Gumbiner BM. Structural elements necessary for oligomerization, trafficking, and cell sorting function of paraxial protocadherin. J Biol Chem. 2007;282:32128–37.",{"doi":902},{"id":898,"text":1057,"url":900,"identifiers":1058},"Rokas A, Krüger D, Carroll SB. Animal evolution and the molecular signature of radiations compressed in time. Science. 2005;310:1933–8.",{"doi":902},{"id":898,"text":1060,"url":900,"identifiers":1061},"Brinkmann H, Philippe H. Animal phylogeny and large-scale sequencing: progress and pitfalls. J Syst Evol. 2008;46:274–86.",{"doi":902},{"id":898,"text":1063,"url":900,"identifiers":1064},"Salichos L, Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 2013;497:327–31.",{"doi":902},{"id":898,"text":1066,"url":900,"identifiers":1067},"Pisani D, Pett W, Dohrmann M, Feuda R, Rota-Stabelli O, Philippe H, et al. Genomic data do not support comb jellies as the sister group to all other animals. Proc Natl Acad Sci U S A. 2015;112:15402–7.",{"doi":902},{"id":1069,"text":1070,"url":1071,"identifiers":1072},"70b3ff28-0082-4978-bc80-c5587a59ee70","Rokas H. Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol. 2000;15:454–9.","https:\u002F\u002Fwww.sciencedirect.com\u002Fscience\u002Farticle\u002Fpii\u002FS0169534700019674",{"doi":1073},"10.1016\u002Fs0169-5347(00)01967-4",{"id":898,"text":1075,"url":900,"identifiers":1076},"Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 2005;6:361–75.",{"doi":902},{"id":898,"text":1078,"url":900,"identifiers":1079},"Delsuc F, Brinkmann H, Chourrout D, Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature. 2006;439:965–8.",{"doi":902},{"id":898,"text":1081,"url":900,"identifiers":1082},"Bourlat SJ, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, Kirschner M, et al. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. Nature. 2006;444:85–8.",{"doi":902},{"id":898,"text":1084,"url":900,"identifiers":1085},"Delsuc F, Tsagkogeorga G, Lartillot N, Philippe H. Additional molecular support for the new chordate phylogeny. Genesis. 2008;46:592–604.",{"doi":902},{"id":898,"text":1087,"url":900,"identifiers":1088},"Friedrich M, Tautz D. Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature. 1995;376:165–7.",{"doi":902},{"id":898,"text":1090,"url":900,"identifiers":1091},"Boore JL, Lavrov DV, Brown WM. Gene translocation links insects and crustaceans. Nature. 1998;392:667–8.",{"doi":902},{"id":898,"text":1093,"url":900,"identifiers":1094},"Shultz JW, Regier JC. Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean + hexapod clade. Proc Biol Sci. 2000;267:1011–9.",{"doi":902},{"id":18,"text":1096,"url":18,"identifiers":1097},"Dohle W. Are the insects terrestrial crustaceans? A discussion of some new facts and arguments and the proposal of the proper name ‘Pancrustacea’ for the monophyletic unit Crustacea+Hexapoda. Ann Soc Entomol. 2001;37:85–103.",{},{"id":898,"text":1099,"url":900,"identifiers":1100},"Giribet G, Edgecombe GD, Wheeler WC. Arthropod phylogeny based on eight molecular loci and morphology. Nature. 2001;413:157–61.",{"doi":902},{"id":898,"text":1102,"url":900,"identifiers":1103},"Meusemann K, von Reumont BM, Simon S, Roeding F, Strauss S, Kück P, et al. A phylogenomic approach to resolve the arthropod tree of life. Mol Biol Evol. 2010;27:2451–64.",{"doi":902},{"id":1105,"text":1106,"url":1107,"identifiers":1108},"f2f5e476-8239-451d-b010-ff980b01b17b","Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, et al. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature. 2010;463:1079–83.","https:\u002F\u002Fwww.nature.com\u002Farticles\u002Fnature08742",{"doi":1109},"10.1038\u002Fnature08742",{"id":1111,"text":1112,"url":1113,"identifiers":1114},"16da901e-7752-49ee-bacf-fdde11c8d814","Timmermans MJ, Roelofs D, Mariën J, van Straalen NM. Revealing pancrustacean relationships: phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers. BMC Evol Biol. 2008;8:83.","http:\u002F\u002Fbmcevolbiol.biomedcentral.com\u002Farticles\u002F10.1186\u002F1471-2148-8-83",{"doi":1115},"10.1186\u002F1471-2148-8-83",{"id":1117,"text":1118,"url":1119,"identifiers":1120},"0a9ee9f6-e483-476c-90c5-d118462f6450","Andrew DR. A new view of insect-crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics. Arthropod Struct Dev. 2011;40:289–302.","https:\u002F\u002Fwww.sciencedirect.com\u002Fscience\u002Farticle\u002Fpii\u002FS1467803911000089",{"doi":1121},"10.1016\u002Fj.asd.2011.02.001",{"id":898,"text":1123,"url":900,"identifiers":1124},"von Reumont BM, Jenner RA, Wills MA, Dell'ampio E, Pass G, Ebersberger I, et al. Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda. Mol Biol Evol. 2012;29:1031–45.",{"doi":902},{"id":898,"text":1126,"url":900,"identifiers":1127},"Oakley TH, Wolfe JM, Lindgren AR, Zaharoff AK. Phylotranscriptomics to bring the understudied into the fold: monophyletic ostracoda, fossil placement, and pancrustacean phylogeny. Mol Biol Evol. 2013;30:215–33.",{"doi":902},{"id":898,"text":1129,"url":900,"identifiers":1130},"Sasaki G, Ishiwata K, Machida R, Miyata T, Su ZH. Molecular phylogenetic analyses support the monophyly of Hexapoda and suggest the paraphyly of Entognatha. BMC Evol Biol. 2013;13:236.",{"doi":902},{"id":898,"text":1132,"url":900,"identifiers":1133},"Jenner RA. Higher-level crustacean phylogeny: consensus and conflicting hypotheses. Arthropod Struct Dev. 2010;39:143–53.",{"doi":902},{"id":898,"text":1135,"url":900,"identifiers":1136},"Giribet G, Edgecombe GD. The Arthropoda: A phylogenetic framework. In Arthropod Biology and Evolution-Molecules, Development, Morphology. Edited by Boxshall G, Fusco G, Minelli A. Berlin: Springer-Verlag; 2013:17–40.",{"doi":902},{"id":898,"text":1138,"url":900,"identifiers":1139},"Harzsch S. The phylogenetic significance of crustacean optic neuropils and chiasmata: a re-examination. J Comp Neurol. 2002;453:10–21.",{"doi":902},{"id":898,"text":1141,"url":900,"identifiers":1142},"Fanenbruck M, Harzsch S, Wägele JW. The brain of the Remipedia (Crustacea) and an alternative hypothesis on their phylogenetic relationships. Proc Natl Acad Sci U S A. 2004;101:3868–73.",{"doi":902},{"id":898,"text":1144,"url":900,"identifiers":1145},"Strausfeld NJ, Andrew DR. A new view of insect-crustacean relationships I. Inferences from neural cladistics and comparative neuroanatomy. Arthropod Struct Dev. 2011;40:276–88.",{"doi":902},{"id":898,"text":1147,"url":900,"identifiers":1148},"Hwang UW, Friedrich M, Tautz D, Park CJ, Kim W. Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature. 2001;413:154–7.",{"doi":902},{"id":898,"text":1150,"url":900,"identifiers":1151},"Lim JT, Hwang UW. The complete mitochondrial genome of Pollicipes Mitella (Crustacea, Maxillopoda, Cirripedia): non-monophylies of maxillopoda and crustacea. Mol Cells. 2006;22:314–22.",{"doi":902},{"id":898,"text":1153,"url":900,"identifiers":1154},"Mallatt J, Giribet G. Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch. Mol Phylogenet Evol. 2006;40:772–94.",{"doi":902},{"id":1156,"text":1157,"url":1158,"identifiers":1159},"cfd3c4ad-7fa5-45e0-add5-f4e3310367e6","Roeding F, Borner J, Kube M, Klages S, Reinhardt R, Burmester T. A 454 sequencing approach for large scale phylogenomic analysis of the common emperor scorpion (Pandinus imperator). Mol Phylogenet Evol. 2009;53:826–34.","https:\u002F\u002Fwww.sciencedirect.com\u002Fscience\u002Farticle\u002Fpii\u002FS1055790309003170",{"doi":1160},"10.1016\u002Fj.ympev.2009.08.014",{"id":898,"text":1162,"url":900,"identifiers":1163},"Rota-Stabelli O, Campbell L, Brinkmann H, Edgecombe GD, Longhorn SJ, Peterson KJ, et al. A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proc Biol Sci. 2011;278:298–306.",{"doi":902},{"id":1165,"text":1166,"url":1167,"identifiers":1168},"9f546b37-345a-49a4-b5b8-d0618887b06a","Regier JC, Shultz JW, Kambic RE. Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proc Biol Sci. 2005;272:395–401.","https:\u002F\u002Froyalsocietypublishing.org\u002Fdoi\u002F10.1098\u002Frspb.2004.2917",{"doi":1169},"10.1098\u002Frspb.2004.2917",{"id":18,"text":1171,"url":18,"identifiers":1172},"Glenner H, Thomsen PF, Hebsgaard MB, Sørensen MV, Willerslev E. Evolution. The origin of insects. Science. 2006;314:1883–4.",{},{"id":898,"text":1174,"url":900,"identifiers":1175},"von Reumont BM, Meusemann K, Szucsich NU, Dell'Ampio E, Gowri-Shankar V, Bartel D, et al. Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships. BMC Evol Biol. 2009;9:119.",{"doi":902},{"id":898,"text":1177,"url":900,"identifiers":1178},"Akiyama-Oda Y, Oda H. Early patterning of the spider embryo: a cluster of mesenchymal cells at the cumulus produces Dpp signals received by germ disc epithelial cells. Development. 2003;130:1735–47.",{"doi":902},{"id":18,"text":1180,"url":1181,"identifiers":1182},"Gott R: Development of gene expression-based biomarkers of exposure to metals and pesticides in the freshwater amphipod Hyalella azteca, 2016, Doctoral dissertation at University of Maryland, Maryland, doi:10.13016\u002FM2PN3J.","https:\u002F\u002Fdrum.lib.umd.edu\u002Fhandle\u002F1903\u002F18263",{"mag":1183,"openalex":1184,"doi":1185},"2495699100","W2495699100","10.13016\u002Fm2pn3j",{"id":898,"text":1187,"url":900,"identifiers":1188},"Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.",{"doi":902},{"id":1190,"createTime":1191,"updateTime":1192,"relativeEntities":1193,"slug":1194,"properties":1195,"entityType":127,"verifyStatus":128,"verifyTime":1205,"verifyNote":130,"languages":18,"translateLanguages":18,"viewCount":19,"primaryUrl":1206,"fullTextUrl":18,"authors":1207,"publicationType":241,"publisherRelationship":1236,"citationCount":18,"citationInfo":18,"publishDate":1260,"publishYear":1261,"citationAnalyzeStatus":350,"lastCitationAnalyze":1262,"indexDatabases":1263,"openAccess":18,"references":18,"isForceReanalyzing":274},"968baa40-6c8b-41dc-8166-34d9cfcc5ab3","2023-12-12T02:40:00.756+00:00","2026-07-26T14:47:20.604+00:00",[],"Evolutionary-biogeography-of-the-centipede-genus-Ethmostigmus-from-Peninsular-India-testing-an-ancient-vicariance-hypothesis-for-Old-World-tropical-diversity",{"abstract":1196,"title":1198,"gsPaper":1200,"references":1201,"doi":1203},{"EN":1197},"Understanding the relative influence of vicariance and dispersal in shaping Old World tropical biodiversity remains a challenge. We aimed to infer the roles of these alternative biogeographic processes using a species time-tree for the centipede genus Ethmostigmus from the Old World tropics. Additionally, we explored fine-scale biogeographic patterns for an endemic radiation of Ethmostigmus from the peninsular Indian Plate (PIP), an area with complex geological and climatic history. Divergence time estimates suggest that Ethmostigmus began diversifying in the Late Cretaceous, 99 (± 25) million years ago (Ma), its early biogeographic history shaped by vicariance. Members of Ethmostigmus in PIP form a monophyletic group that underwent endemic radiation in the Late Cretaceous, 72 (± 25) Ma. In contrast, a new species of Ethmostigmus from north-east India formed a clade with African\u002FAustralian species. Fine-scale biogeographic analyses in PIP predict that Indian Ethmostigmus had an ancestor in southern-central parts of the Western Ghats. This was followed by four independent dispersal events from the southern-central Western Ghats to the Eastern Ghats, and between different parts of the Western Ghats in the Cenozoic. Our results are consistent with Gondwanan break-up driving the early evolutionary history of the genus Ethmostigmus. Multiple dispersal events coinciding with geo-climatic events throughout the Cenozoic shaped diversification in PIP. Ethmostigmus species in PIP are restricted to wet forests and have retained that niche throughout their diversification.",{"EN":1199},"Evolutionary biogeography of the centipede genus Ethmostigmus from Peninsular India: testing an ancient vicariance hypothesis for Old World tropical diversity",{"VOID":287},{"VOID":1202},"Wiens JJ, Donoghue MJ. Historical biogeography, ecology and species richness. Trends Ecol Evol. 2004;19(12):639–44.\nWiens JJ, Sukumaran J, Pyron RA, Brown RM. Evolutionary and biogeographic origins of high tropical diversity in old world frogs (Ranidae). Evolution. 2009;63(5):1217–31.\nCox CB, Ladle R, Moore PD. Biogeography: an ecological and evolutionary approach. 8th ed. Hoboken, NJ: John Wiley & Sons; 2016.\nLomolino M, Riddle B, Brown J. Biogeography. 3rd ed. Sunderland, MA: Sinauer Associates; 2006.\nSanmartin I, Ronquist F. Southern hemisphere biogeography inferred by event-based models: plant versus animal patterns. Syst Biol. 2004;53(2):216–43.\nStorey BC. The role of mantle plumes in continental breakup: case histories from Gondwanaland. Nature. 1995;377:301.\nGamble T, Bauer AM, Greenbaum E, Jackman TR. Evidence for Gondwanan vicariance in an ancient clade of gecko lizards. J Biogeogr. 2008;35(1):88–104.\nThomas N, Bruhl JJ, Ford A, Weston PH, Ebach M. Molecular dating of Winteraceae reveals a complex biogeographical history involving both ancient Gondwanan vicariance and long-distance dispersal. J Biogeogr. 2014;41(5):894–904.\nClaramunt S, Cracraft J. A new time tree reveals earth history’s imprint on the evolution of modern birds. Sci Adv. 2015;1(11):e1501005.\nToussaint EFA, Bloom D, Short AEZ. Cretaceous West Gondwana vicariance shaped giant water scavenger beetle biogeography. J Biogeogr. 2017;44(9):1952–65.\nWaters JM, Roy MS, Crandall K. Out of Africa: the slow train to Australasia. Syst Biol. 2004;53(1):18–24.\nBartish IV, Antonelli A, Richardson JE, Swenson U. Vicariance or long-distance dispersal: historical biogeography of the pantropical subfamily Chrysophylloideae (Sapotaceae). J Biogeogr. 2011;38(1):177–90.\nKainulainen K, Razafimandimbison SG, Wikström N, Bremer B. Island hopping, long-distance dispersal and species radiation in the Western Indian Ocean: historical biogeography of the Coffeeae alliance (Rubiaceae). J Biogeogr. 2017;44(9):1966–79.\nRenner SS, Strijk JS, Strasberg D, Thébaud C. Biogeography of the Monimiaceae (Laurales): a role for East Gondwana and long-distance dispersal, but not West Gondwana. J Biogeogr. 2010;37(7):1227–38.\nClayton JW, Soltis PS, Soltis DE. Recent long-distance dispersal overshadows ancient biogeographical patterns in a pantropical angiosperm family (Simaroubaceae, Sapindales). Syst Biol. 2009;58(4):395–410.\nMuellner AN, Savolainen V, Samuel R, Chase MW. The mahogany family “out-of-Africa”: divergence time estimation, global biogeographic patterns inferred from plastid rbcL DNA sequences, extant, and fossil distribution of diversity. Mol Phylogenet Evol. 2006;40(1):236–50.\nToussaint EFA, Short AEZ. Biogeographic mirages? Molecular evidence for dispersal-driven evolution in Hydrobiusini water scavenger beetles. Syst Entomol. 2017;42(4):692–702.\nCrisp MD, Cook LG. How was the Australian flora assembled over the last 65 million years? A molecular phylogenetic perspective. Annu Rev Ecol Evol Syst. 2013;44:303–24.\nLuebert F, Couvreur TL, Gottschling M, Hilger HH, Miller JS, Weigend M. Historical biogeography of Boraginales: west Gondwanan vicariance followed by long-distance dispersal? J Biogeogr. 2017;44(1):158–69.\nEdgecombe GD. Chilopoda–the fossil history. In: Treatise on zoology—anatomy, taxonomy, biology. The Myriapoda. Vol. 1; 2011: 355–361.\nPocock RI. List of the Arachnida and ‘Myriapoda’ obtained in Funafuti by prof. W. J. Sollas and Mr. Stanley Gardiner, and in Rotuma by Mr. Stanley Gardiner. Annals and Magazine of Natural History, Series. 1898;7(1):321–9.\nBonato L, Chagas Jr A, Edgecombe G, Lewis J, Minelli A, Pereira L, Shelley R, Stoev P, Zapparoli M. ChiloBase 2.0–A World Catalogue of Centipedes (Chilopoda). In: Available online at: http:\u002F\u002Fchilobase.biologia.unipd.it [Accessed 09\u002F04\u002F2016]. 2016.\nJoshi J, Edgecombe G. Molecular phylogeny and systematics of the centipede genus Ethmostigmus Pocock, 1898 (Chilopoda: Scolopendromorpha) from peninsular India. Invertebr Syst. 2018;32:1316–35.\nKoch LE. A taxonomic study of the centipede genus Ethmostigmus Pocock (Chilopoda: Scolopendridae: Otostigminae) in Australia. Aust J Zool. 1983;31(5):835–49.\nSchileyko A, Stagl V. The collection of scolopendromorph centipedes (Chilopoda) in the Natural History Museum in Vienna: a critical re-evaluation of former taxonomic identifications. Ann Nat Hist Mus Wien. 2004;105:67–137.\nSchileyko AA, Stoev PE. Scolopendromorpha of New Guinea and adjacent islands (Myriapoda, Chilopoda). Zootaxa. 2016;4147(3):247–80.\nSimaiakis SM, Edgecombe GD. Scolopendromorph centipedes (Chilopoda: Scolopendromorpha) in the Natural History Museum (London): a review of the hitherto unidentified species collected in Africa, with remarks on taxonomy and distribution, and a new species of Otostigmus (Parotostigmus). Zootaxa. 2013;3734(2):169–98.\nJoshi J, Karanth KP. Cretaceous–tertiary diversification among select scolopendrid centipedes of South India. Mol Phylogenet Evol. 2011;60(3):287–94.\nChatterjee S, Scotese CR. The breakup of Gondwana and the evolution and biogeography of the Indian plate. Indian Nat Sci Acad Part A. 1999;65(3):397–426.\nSingh R, Kar R, Prasad G. Palynological constraints on the age of mammal-yielding Deccan intertrappean beds of Naskal, Rangareddi district. Andhra Pradesh Curr Sci. 2006:1281–5.\nSamant B, Mohabey D. Palynoflora from Deccan volcano-sedimentary sequence (Cretaceous-Palaeogene transition) of Central India: implications for spatio-temporal correlation. J Biosci. 2009;34(5):811–23.\nJoshi J, Karanth P. Did southern Western Ghats of peninsular India serve as refugia for its endemic biota during the Cretaceous volcanism? Ecol Evol. 2013;3(10):3275–82.\nPrasad V, Farooqui A, Tripathi S, Garg R, Thakur B. Evidence of late Palaeocene-early Eocene equatorial rain forest refugia in southern Western Ghats, India. J Biosci. 2009;34(5):777.\nAgarwal I, Bauer AM, Jackman TR, Karanth KP. Insights into Himalayan biogeography from geckos: a molecular phylogeny of Cyrtodactylus (Squamata: Gekkonidae). Mol Phylogenet Evol. 2014;80:145–55.\nAgarwal I, Karanth KP. A phylogeny of the only ground-dwelling radiation of Cyrtodactylus (Squamata, Gekkonidae): diversification of Geckoella across peninsular India and Sri Lanka. Mol Phylogenet Evol. 2015;82:193–9.\nAgarwal I, Ramakrishnan U. A phylogeny of open-habitat lizards (Squamata: Lacertidae: Ophisops) supports the antiquity of Indian grassy biomes. J Biogeogr. 2017;44(9):2021–32.\nDeepak V, Karanth P. Aridification driven diversification of fan-throated lizards from the Indian subcontinent. Mol Phylogenet Evol. 2018;120:53–62.\nBansal R, Karanth KP. Molecular phylogeny of Hemidactylus geckos (Squamata: Gekkonidae) of the Indian subcontinent reveals a unique Indian radiation and an Indian origin of Asian house geckos. Mol Phylogenet Evol. 2010;57(1):459–65.\nDatta-Roy A, Singh M, Karanth KP. Phylogeny of endemic skinks of the genus Lygosoma (Squamata: Scincidae) from India suggests an in situ radiation. J Genet. 2014;93(1):163–7.\nDatta-Roy A, Singh M, Srinivasulu C, Karanth KP. Phylogeny of the Asian Eutropis (Squamata: Scincidae) reveals an ‘into India’endemic Indian radiation. Mol Phylogenet Evol. 2012;63(3):817–24.\nGower DJ, Agarwal I, Karanth KP, Datta-Roy A, Giri VB, Wilkinson M, San Mauro D. The role of wet-zone fragmentation in shaping biodiversity patterns in peninsular India: insights from the caecilian amphibian Gegeneophis. J Biogeogr. 2016;43(6):1091–102.\nCyriac VP, Kodandaramaiah U. Paleoclimate determines diversification patterns in the fossorial snake family Uropeltidae Cuvier, 1829. Mol Phylogenet Evol. 2017;116:97–107.\nWilson HM. A new scolopendromorph centipede (Myriapoda: Chilopoda) from the lower Cretaceous (Aptian) of Brazil. J Paleontol. 2003;77(1):73–7.\nWolfe JM, Daley AC, Legg DA, Edgecombe GD. Fossil calibrations for the arthropod tree of life. Earth-Sci Rev. 2016;160:43–110.\nFernández R, Edgecombe GD, Giribet G. Exploring phylogenetic relationships within Myriapoda and the effects of matrix composition and occupancy on phylogenomic reconstruction. Syst Biol. 2016;65(5):871–89.\nEdgecombe G, Giribet G. Adding mitochondrial sequence data (16S rRNA and cytochrome c oxidase subunit I) to the phylogeny of centipedes (Myriapoda: Chilopoda): an analysis of morphology and four molecular loci. J Zool Syst Evol Res. 2004;42(2):89–134.\nShear WA, Bonamo PM. Devonobiomorpha, a new order of centipeds (Chilopoda) from the Middle Devonian of Gilboa, New York State, USA, and the phylogeny of centiped orders. American Museum novitates; no. 2927. 1988.\nSchenk JJ. Consequences of secondary calibrations on divergence time estimates. PLoS One. 2016;11(1):e0148228.\nEdgecombe GD, Giribet G. A New Zealand species of the trans-Tasman centipede order Craterostigmomorpha (Arthropoda: Chilopoda) corroborated by molecular evidence. Invertebr Syst. 2008;22(1):1–15.\nGiribet G, Carranza S, Riutort M, Baguñà J, Ribera C. Internal phylogeny of the Chilopoda (Myriapoda, Arthropoda) using complete 18S rDNA and partial 28S rDNA sequences. Philos Trans R Soc Lond Ser B Biol Sci. 1999;354(1380):215–22.\nGiribet G, Edgecombe GD, Wheeler WC. Arthropod phylogeny based on eight molecular loci and morphology. Nature. 2001;413(6852):157.\nHwang UW, Friedrich M, Tautz D, Park CJ, Kim W. Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature. 2001;413(6852):154.\nJoshi J, Karanth KP. Coalescent method in conjunction with niche modeling reveals cryptic diversity among centipedes in the Western Ghats of South India. PLoS One. 2012;7(8):1–12.\nMurienne J, Edgecombe GD, Giribet G. Including secondary structure, fossils and molecular dating in the centipede tree of life. Mol Phylogenet Evol. 2010;57(1):301–13.\nSiriwut W, Edgecombe GD, Sutcharit C, Panha S. The centipede genus Scolopendra in mainland Southeast Asia: molecular phylogenetics, geometric morphometrics and external morphology as tools for species delimitation. PLoS One. 2015;10(8):e0135355.\nSiriwut W, Edgecombe GD, Sutcharit C, Tongkerd P, Panha S. First record of the African-Indian centipede genus Digitipes Attems, 1930 (Scolopendromorpha: Otostigminae) from Myanmar, and the systematic position of a new species based on molecular phylogenetics. Zootaxa. 2015;3931(1):71–87.\nSiriwut W, Edgecombe GD, Sutcharit C, Tongkerd P, Panha S. Systematic revision and phylogenetic reassessment of the centipede genera Rhysida wood, 1862 and Alluropus Silvestri, 1911 (Chilopoda: Scolopendromorpha) in Southeast Asia, with further discussion of the subfamily Otostigminae. Invertebr Syst. 2018. https:\u002F\u002Fdoi.org\u002F10.1071\u002FIS17081.\nVahtera V, Edgecombe GD. First molecular data and the phylogenetic position of the millipede-like centipede Edentistoma octosulcatum Tömösvary, 1882 (Chilopoda: Scolopendromorpha: Scolopendridae). PLoS One. 2014;9(11):e112461.\nVahtera V, Edgecombe GD, Giribet G. Evolution of blindness in scolopendromorph centipedes (Chilopoda: Scolopendromorpha): insight from an expanded sampling of molecular data. Cladistics. 2012;28(1):4–20.\nVahtera V, Edgecombe GD, Giribet G. Phylogenetics of scolopendromorph centipedes: can denser taxon sampling improve an artificial classification? Invertebr Syst. 2013;27(5):578–602.\nThompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673–80.\nKatoh K, Misawa K, Ki K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30(14):3059–66.\nHeled J, Drummond AJ. Bayesian inference of species trees from multilocus data. Mol Biol Evol. 2009;27(3):570–80.\nMiller MA, Pfeiffer W, Schwartz T. Creating the CIPRES science gateway for inference of large phylogenetic trees. In: Gateway Computing Environments Workshop (GCE), 2010: 2010. Ieee: 1–8.\nMatzke NJ. Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades. Syst Biol. 2014;63(6):951–70.\nPirie MD, Litsios G, Bellstedt DU, Salamin N, Kissling J. Back to Gondwanaland: can ancient vicariance explain (some) Indian Ocean disjunct plant distributions? Biol Lett. 2015;11(6):20150086.\nToussaint EFA, Fikáček M, Short AE. India–Madagascar vicariance explains cascade beetle biogeography. Biol J Linnean Soc. 2016;118(4):982–91.\nAduse-Poku K, Brattstrom O, Kodandaramaiah U, Lees DC, Brakefield PM, Wahlberg N. Systematics and historical biogeography of the old world butterfly subtribe Mycalesina (Lepidoptera: Nymphalidae: Satyrinae). BMC Evol Biol. 2015;15:167.\nDatta-Roy A, Praveen Karanth K. The out-of-India hypothesis: what do molecules suggest? J Biosci. 2009;34(5):687–97.\nBiju SD, Bossuyt F. New frog family from India reveals an ancient biogeographical link with the Seychelles. Nature. 2003;425:711.\nVan Bocxlaer I, Biju SD, Willaert B, Giri VB, Shouche YS, Bossuyt F. Mountain-associated clade endemism in an ancient frog family (Nyctibatrachidae) on the Indian subcontinent. Mol Phylogenet Evol. 2012;62(3):839–47.\nAgarwal I, Dutta-Roy A, Bauer AM, Giri VB. Rediscovery of Geckoella jeyporensis (Squamata: Gekkonidae), with notes on morphology, coloration and habitat. Hamadryad. 2012;36:17–24.\nDeepak V, Giri VB, Asif M, Dutta SK, Vyas R, Zambre AM, Bhosale H, Karanth KP. Systematics and phylogeny of Sitana (Reptilia: Agamidae) of peninsular India, with the description of one new genus and five new species. Contributions Zool. 2016;85(1):67–111.\nSpicer RA. Tibet, the Himalaya, Asian monsoons and biodiversity-in what ways are they related? Plant Divers. 2017;39:233–44.\nMorley RJ. Origin and evolution of tropical rain forests: John Wiley & Sons; Chichester 2000.\nShukla A, Mehrotra R, Guleria J. Emergence and extinction of Dipterocarpaceae in western India with reference to climate change: fossil wood evidences. J Earth Syst Sci. 2013;122(5):1373–86.\nMorley RJ. Cretaceous and Tertiary climate change and the past distribution of megathermal rainforests. Tropical rainforest responses to climatic change: (ed. by M.B. Bush and J.R. Flenley). Springer; Berlin. 2007. p. 1–31.\nZachos J, Pagani M, Sloan L, Thomas E, Billups K. Trends, rhythms, and aberrations in global climate 65 ma to present. Science. 2001;292(5517):686–93.\nVijayakumar S, Menezes RC, Jayarajan A, Shanker K. Glaciations, gradients, and geography: multiple drivers of diversification of bush frogs in the Western Ghats escarpment. Proc R Soc B. 2016;283(1836):20161011.\nMinelli A. Treatise on Zoology–The Myriapoda Volume. 2011;1:363–443.",{"VOID":1204},"10.1186\u002Fs12862-019-1367-6","2024-08-31T01:27:00.752+00:00","https:\u002F\u002Fbmcevolbiol.biomedcentral.com\u002Farticles\u002F10.1186\u002Fs12862-019-1367-6",[1208,1223],{"id":1209,"sortIndex":19,"researcher":18,"roles":1210,"affiliations":1211,"properties":1220},"80aa1053-3d8e-4fbb-9dbb-80b837a40509",[136],[1212],{"id":1213,"sortIndex":19,"affiliation":1214,"properties":18},"0e3bdefe-1038-46fe-80cd-ac8f78af5b05",{"id":1213,"createTime":18,"updateTime":18,"relativeEntities":1215,"slug":18,"properties":1216,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1219,"statistic":18},[],{"title":1217},{"VI":1218},"The Natural History Museum, London, UK",[],{"title":1221},{"VI":1222},"Jahnavi Joshi",{"id":1224,"sortIndex":148,"researcher":18,"roles":1225,"affiliations":1226,"properties":1233},"de78bd6f-a52e-4e7a-bae3-62392dd968ca",[136],[1227],{"id":1213,"sortIndex":19,"affiliation":1228,"properties":18},{"id":1213,"createTime":18,"updateTime":18,"relativeEntities":1229,"slug":18,"properties":1230,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1232,"statistic":18},[],{"title":1231},{"VI":1218},[],{"title":1234},{"VI":1235},"Gregory D. Edgecombe",{"url":1206,"publisher":1237,"properties":1256},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":1238,"slug":10,"properties":1239,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":1242,"manageAffiliations":1243,"indexDatabases":1244,"url":18,"thumbnailPath":18,"statistic":1251,"gsStatistic":18,"type":18,"analyzePriority":18},[],{"title":1240,"eissn":1241},{"EN":13},{"VOID":15},[],[],[1245],{"id":24,"indexDatabase":1246,"url":35,"indexYears":36,"academicFieldIds":18,"indexDatabaseRanking":37},{"id":26,"createTime":18,"updateTime":18,"relativeEntities":1247,"label":1248,"description":1249,"key":32,"publicationTags":1250,"standard":18},[],{"EN":29,"VI":29},{"EN":29,"VI":31},[34],{"impactFactor":19,"impactFactorByYear":1252,"i10Index":51,"i10IndexLast5Year":52,"totalPublication":53,"totalPublicationByYear":1253,"totalCitation":70,"totalCitationByYear":1254,"totalCitationPerPublication":88,"totalCitationPerPublicationByYear":1255,"hindexLast5Year":105,"hindex":105},{"2012":40,"2013":41,"2014":42,"2015":43,"2016":44,"2017":45,"2018":46,"2019":47,"2020":48,"2021":49,"2022":50},{"2005":55,"2006":56,"2007":57,"2008":58,"2009":59,"2010":60,"2011":61,"2012":62,"2013":63,"2014":64,"2015":65,"2016":66,"2017":67,"2018":68,"2019":69,"2020":62},{"2005":72,"2006":73,"2007":74,"2008":75,"2009":76,"2010":77,"2011":78,"2012":79,"2013":80,"2014":81,"2015":82,"2016":83,"2017":84,"2018":85,"2019":86,"2020":87},{"2005":90,"2006":91,"2007":92,"2008":93,"2009":94,"2010":95,"2011":96,"2012":97,"2013":98,"2014":52,"2015":99,"2016":100,"2017":101,"2018":102,"2019":103,"2020":104},{"pages":1257,"volume":1258},{"VOID":770},{"VOID":1259},"19","2019-02-01",2019,"2026-07-26T14:47:20.603+00:00",[37],{"id":1265,"createTime":1266,"updateTime":1267,"relativeEntities":1268,"slug":1269,"properties":1270,"entityType":127,"verifyStatus":128,"verifyTime":1281,"verifyNote":130,"languages":18,"translateLanguages":18,"viewCount":19,"primaryUrl":1282,"fullTextUrl":18,"authors":1283,"publicationType":241,"publisherRelationship":1390,"citationCount":19,"citationInfo":1415,"publishDate":1417,"publishYear":637,"citationAnalyzeStatus":709,"lastCitationAnalyze":1418,"indexDatabases":1419,"openAccess":18,"references":18,"isForceReanalyzing":274},"25933f07-4420-45ce-8166-324d0526b900","2023-12-01T05:40:18.535+00:00","2026-07-26T14:30:46.646+00:00",[],"Sox-genes-in-the-coral-Acropora-millepora-divergent-expression-patterns-reflect-differences-in-developmental-mechanisms-within-the-Anthozoa",{"abstract":1271,"title":1273,"gsPaper":1275,"references":1277,"doi":1279},{"EN":1272},"Sox genes encode transcription factors that function in a wide range of developmental processes across the animal kingdom. To better understand both the evolution of the Sox family and the roles of these genes in cnidarians, we are studying the Sox gene complement of the coral, Acropora millepora (Class Anthozoa). Based on overall domain structures and HMG box sequences, the Acropora Sox genes considered here clearly fall into four of the five major Sox classes. AmSoxC is expressed in the ectoderm during development, in cells whose morphology is consistent with their assignment as sensory neurons. The expression pattern of the Nematostella ortholog of this gene is broadly similar to that of AmSoxC, but there are subtle differences – for example, expression begins significantly earlier in Acropora than in Nematostella. During gastrulation, AmSoxBb and AmSoxB1 transcripts are detected only in the presumptive ectoderm while AmSoxE1 transcription is restricted to the presumptive endoderm, suggesting that these Sox genes might play roles in germ layer specification. A third type B Sox gene, AmSoxBa, and a Sox F gene AmSoxF also have complex and specific expression patterns during early development. Each of these genes has a clear Nematostella ortholog, but in several cases the expression pattern observed in Acropora differs significantly from that reported in Nematostella. These differences in expression patterns between Acropora and Nematostella largely reflect fundamental differences in developmental processes, underscoring the diversity of mechanisms within the anthozoan Sub-Class Hexacorallia (Zoantharia).",{"EN":1274},"Sox genes in the coral Acropora millepora: divergent expression patterns reflect differences in developmental mechanisms within the Anthozoa",{"VOID":1276},"[\"5979806027191284396\"]",{"VOID":1278},"Schepers GE, Teasdale RD, Koopman P: Twenty pairs of sox: extent, homology, and nomenclature of the mouse and human sox transcription factor gene families. Dev Cell. 2002, 3 (2): 167-170. 10.1016\u002FS1534-5807(02)00223-X.\nBowles J, Schepers G, Koopman P: Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev Biol. 2000, 227 (2): 239-255. 10.1006\u002Fdbio.2000.9883.\nCremazy F, Berta P, Girard F: Genome-wide analysis of Sox genes in Drosophila melanogaster. Mech Dev. 2001, 109 (2): 371-375. 10.1016\u002FS0925-4773(01)00529-9.\nWegner M: From head to toes: the multiple facets of Sox proteins. Nucleic Acids Res. 1999, 27 (6): 1409-1420. 10.1093\u002Fnar\u002F27.6.1409.\nMcKimmie C, Woerfel G, Russell S: Conserved genomic organisation of Group B Sox genes in insects. BMC Genet. 2005, 6 (1): 26-10.1186\u002F1471-2156-6-26.\nJager M, Queinnec E, Houliston E, Manuel M: Expansion of the SOX gene family predated the emergence of the Bilateria. Mol Phylogenet Evol. 2006, 39 (2): 468-477. 10.1016\u002Fj.ympev.2005.12.005.\nLarroux C, Fahey B, Liubicich D, Hinman VF, Gauthier M, Gongora M, Green K, Worheide G, Leys SP, Degnan BM: Developmental expression of transcription factor genes in a demosponge: insights into the origin of metazoan multicellularity. Evol Dev. 2006, 8 (2): 150-173. 10.1111\u002Fj.1525-142X.2006.00086.x.\nLarroux C, Luke GN, Koopman P, Rokhsar DS, Shimeld SM, Degnan BM: Genesis and expansion of metazoan transcription factor gene classes. Mol Biol Evol. 2008, 25 (5): 980-996. 10.1093\u002Fmolbev\u002Fmsn047.\nMagie CR, Pang K, Martindale MQ: Genomic inventory and expression of Sox and Fox genes in the cnidarian Nematostella vectensis. Dev Genes Evol. 2005, 215 (12): 618-630. 10.1007\u002Fs00427-005-0022-y.\nSrivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, et al: The Trichoplax genome and the nature of placozoans. Nature. 2008, 454 (7207): 955-960. 10.1038\u002Fnature07191.\nGubbay J, Collignon J, Koopman P, Capel B, Economou A, Munsterberg A, Vivian N, Goodfellow P, Lovell-Badge R: A gene mapping to the sex-determining region of the mouse Y chromosome is a member of a novel family of embryonically expressed genes. Nature. 1990, 346 (6281): 245-250. 10.1038\u002F346245a0.\nSinclair AH, Berta P, Palmer MS, Hawkins JR, Griffiths BL, Smith MJ, Foster JW, Frischauf AM, Lovell-Badge R, Goodfellow PN: A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif. Nature. 1990, 346 (6281): 240-244. 10.1038\u002F346240a0.\nBuescher M, Hing FS, Chia W: Formation of neuroblasts in the embryonic central nervous system of Drosophila melanogaster is controlled by SoxNeuro. Development. 2002, 129 (18): 4193-4203.\nMizuseki K, Kishi M, Matsui M, Nakanishi S, Sasai Y: Xenopus Zic-related-1 and Sox-2, two factors induced by chordin, have distinct activities in the initiation of neural induction. Development. 1998, 125 (4): 579-587.\nOverton PM, Meadows LA, Urban J, Russell S: Evidence for differential and redundant function of the Sox genes Dichaete and SoxN during CNS development in Drosophila. Development. 2002, 129 (18): 4219-4228.\nCremazy F, Berta P, Girard F: Sox neuro, a new Drosophila Sox gene expressed in the developing central nervous system. Mech Dev. 2000, 93 (1–2): 215-219. 10.1016\u002FS0925-4773(00)00268-9.\nHolland LZ, Schubert M, Holland ND, Neuman T: Evolutionary conservation of the presumptive neural plate markers AmphiSox1\u002F2\u002F3 and AmphiNeurogenin in the invertebrate chordate amphioxus. Dev Biol. 2000, 226 (1): 18-33. 10.1006\u002Fdbio.2000.9810.\nLe Gouar M, Guillou A, Vervoort M: Expression of a SoxB and a Wnt2\u002F13 gene during the development of the mollusc Patella vulgata. Dev Genes Evol. 2004, 214 (5): 250-256. 10.1007\u002Fs00427-004-0399-z.\nLowe CJ, Wu M, Salic A, Evans L, Lander E, Stange-Thomann N, Gruber CE, Gerhart J, Kirschner M: Anteroposterior patterning in hemichordates and the origins of the chordate nervous system. Cell. 2003, 113 (7): 853-865. 10.1016\u002FS0092-8674(03)00469-0.\nMiya T, Nishida H: Expression pattern and transcriptional control of SoxB1 in embryos of the ascidian Halocynthia roretzi. Zoolog Sci. 2003, 20 (1): 59-67. 10.2108\u002Fzsj.20.59.\nTaguchi S, Tagawa K, Humphreys T, Satoh N: Group B sox genes that contribute to specification of the vertebrate brain are expressed in the apical organ and ciliary bands of hemichordate larvae. Zoolog Sci. 2002, 19 (1): 57-66. 10.2108\u002Fzsj.19.57.\nZhang C, Basta T, Hernandez-Lagunas L, Simpson P, Stemple DL, Artinger KB, Klymkowsky MW: Repression of nodal expression by maternal B1-type SOXs regulates germ layer formation in Xenopus and zebrafish. Dev Biol. 2004, 273 (1): 23-37. 10.1016\u002Fj.ydbio.2004.05.019.\nKenny AP, Oleksyn DW, Newman LA, Angerer RC, Angerer LM: Tight regulation of SpSoxB factors is required for patterning and morphogenesis in sea urchin embryos. Dev Biol. 2003, 261 (2): 412-425. 10.1016\u002FS0012-1606(03)00331-2.\nMiller DJ, Ball EE: Cryptic complexity captured: the Nematostella genome reveals its secrets. Trends Genet. 2008, 24 (1): 1-4. 10.1016\u002Fj.tig.2007.10.002.\nChevalier S, Martin A, Leclere L, Amiel A, Houliston E: Polarised expression of FoxB and FoxQ2 genes during development of the hydrozoan Clytia hemisphaerica. Dev Genes Evol. 2006, 216 (11): 709-720. 10.1007\u002Fs00427-006-0103-6.\nByrum CA, Martindale MQ: Gastrulation in the Cnidaria and Ctenophora. In C. D. Stern (ed.). Gastrulation: From Cells to Embryo. 2004, Cold Spring Harbor Laboratory Press, 33-50.\nKortschak RD, Samuel G, Saint R, Miller DJ: EST analysis of the cnidarian Acropora millepora reveals extensive gene loss and rapid sequence divergence in the model invertebrates. Curr Biol. 2003, 13 (24): 2190-2195. 10.1016\u002Fj.cub.2003.11.030.\nTechnau U, Rudd S, Maxwell P, Gordon PM, Saina M, Grasso LC, Hayward DC, Sensen CW, Saint R, Holstein TW, et al: Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians. Trends Genet. 2005, 21 (12): 633-639. 10.1016\u002Fj.tig.2005.09.007.\nSinner D, Rankin S, Lee M, Zorn AM: Sox17 and beta-catenin cooperate to regulate the transcription of endodermal genes. Development. 2004, 131 (13): 3069-3080. 10.1242\u002Fdev.01176.\nKamachi Y, Uchikawa M, Collignon J, Lovell-Badge R, Kondoh H: Involvement of Sox1, 2 and 3 in the early and subsequent molecular events of lens induction. Development. 1998, 125 (13): 2521-2532.\nWetering van de M, Oosterwegel M, van Norren K, Clevers H: Sox-4, an Sry-like HMG box protein, is a transcriptional activator in lymphocytes. Embo J. 1993, 12 (10): 3847-3854.\nde Jong DM, Hislop NR, Hayward DC, Reece-Hoyes JS, Pontynen PC, Ball EE, Miller DJ: Components of both major axial patterning systems of the Bilateria are differentially expressed along the primary axis of a 'radiate' animal, the anthozoan cnidarian Acropora millepora. Dev Biol. 2006, 298 (2): 632-643. 10.1016\u002Fj.ydbio.2006.07.034.\nHayward DC, Catmull J, Reece-Hoyes JS, Berghammer H, Dodd H, Hann SJ, Miller DJ, Ball EE: Gene structure and larval expression of cnox-2Am from the coral Acropora millepora. Dev Genes Evol. 2001, 211 (1): 10-19. 10.1007\u002Fs004270000112.\nLi M, Zhao C, Wang Y, Zhao Z, Meng A: Zebrafish sox9b is an early neural crest marker. Dev Genes Evol. 2002, 212 (4): 203-206. 10.1007\u002Fs00427-002-0235-2.\nMcCauley DW, Bronner-Fraser M: Importance of SoxE in neural crest development and the evolution of the pharynx. Nature. 2006, 441 (7094): 750-752. 10.1038\u002Fnature04691.\nSpokony RF, Aoki Y, Saint-Germain N, Magner-Fink E, Saint-Jeannet JP: The transcription factor Sox9 is required for cranial neural crest development in Xenopus. Development. 2002, 129 (2): 421-432.\nJuliano CE, Voronina E, Stack C, Aldrich M, Cameron AR, Wessel GM: Germ line determinants are not localized early in sea urchin development, but do accumulate in the small micromere lineage. Dev Biol. 2006, 300 (1): 406-415. 10.1016\u002Fj.ydbio.2006.07.035.\nBall EE, Hayward DC, Reece-Hoyes JS, Hislop NR, Samuel G, Saint R, Harrison PL, Miller DJ: Coral development: from classical embryology to molecular control. Int J Dev Biol. 2002, 46 (4): 671-678.\nBall EE, Hayward DC, Saint R, Miller DJ: A simple plan – cnidarians and the origins of developmental mechanisms. Nat Rev Genet. 2004, 5 (8): 567-577. 10.1038\u002Fnrg1402.\nFritzenwanker JH, Genikhovich G, Kraus Y, Technau U: Early development and axis specification in the sea anemone Nematostella vectensis. Dev Biol. 2007, 310 (2): 264-279. 10.1016\u002Fj.ydbio.2007.07.029.\nKraus Y, Technau U: Gastrulation in the sea anemone Nematostella vectensis occurs by invagination and immigration: an ultrastructural study. Dev Genes Evol. 2006, 216 (3): 119-132. 10.1007\u002Fs00427-005-0038-3.\nMagie CR, Daly M, Martindale MQ: Gastrulation in the cnidarian Nematostella vectensis occurs via invagination not ingression. Dev Biol. 2007, 305 (2): 483-497. 10.1016\u002Fj.ydbio.2007.02.044.\nHand C, Uhlinger KR: The culture, sexual and asexual reproduction, and growth of the sea anemone Nematostella vectensis. Biol Bull. 1992, 182: 169-176. 10.2307\u002F1542110.\nHayward DC, Samuel G, Pontynen PC, Catmull J, Saint R, Miller DJ, Ball EE: Localized expression of a dpp\u002FBMP2\u002F4 ortholog in a coral embryo. Proc Natl Acad Sci USA. 2002, 99 (12): 8106-8111. 10.1073\u002Fpnas.112021499.\nOkubo N, Motokawa T: Embryogenesis in the reef-building coral Acropora spp. Zoolog Sci. 2007, 24 (12): 1169-1177. 10.2108\u002Fzsj.24.1169.\nFritzenwanker JH, Technau U: Induction of gametogenesis in the basal cnidarian Nematostella vectensis(Anthozoa). Dev Genes Evol. 2002, 212 (2): 99-103. 10.1007\u002Fs00427-002-0214-7.\nKusserow A, Pang K, Sturm C, Hrouda M, Lentfer J, Schmidt HA, Technau U, von Haeseler A, Hobmayer B, Martindale MQ, et al: Unexpected complexity of the Wnt gene family in a sea anemone. Nature. 2005, 433 (7022): 156-160. 10.1038\u002Fnature03158.\nMiller SW, Hayward DC, Bunch TA, Miller DJ, Ball EE, Bardwell VJ, Zarkower D, Brower DL: A DM domain protein from a coral, Acropora millepora, homologous to proteins important for sex determination. Evol Dev. 2003, 5 (3): 251-258. 10.1046\u002Fj.1525-142X.2003.03032.x.\nAdachi J, Hasegawa M: MOLPHY version 2.3: program for molecular phylogenetic based on maximum likelihood. Comput Sci Monogr. 1996, 28: 1-150.\nLaudet V, Stehelin D, Clevers H: Ancestry and diversity of the HMG box superfamily. Nucleic Acids Res. 1993, 21 (10): 2493-2501. 10.1093\u002Fnar\u002F21.10.2493.\nHobmayer B, Rentzsch F, Kuhn K, Happel CM, von Laue CC, Snyder P, Rothbacher U, Holstein TW: WNT signalling molecules act in axis formation in the diploblastic metazoan Hydra. Nature. 2000, 407 (6801): 186-189. 10.1038\u002F35025063.\nAnctil M, Hayward DC, Miller DJ, Ball EE: Sequence and expression of four coral G protein-coupled receptors distinct from all classifiable members of the rhodopsin family. Gene. 2007, 392 (1–2): 14-21. 10.1016\u002Fj.gene.2006.10.025.\nScholz CB, Technau U: The ancestral role of Brachyury: expression of NemBra1 in the basal cnidarian Nematostella vectensis (Anthozoa). Dev Genes Evol. 2003, 212 (12): 563-570.",{"VOID":1280},"10.1186\u002F1471-2148-8-311","2024-08-31T03:19:23.974+00:00","https:\u002F\u002Fbmcevolbiol.biomedcentral.com\u002Farticles\u002F10.1186\u002F1471-2148-8-311",[1284,1309,1332,1347,1364,1377],{"id":1285,"sortIndex":19,"researcher":18,"roles":1286,"affiliations":1287,"properties":1304},"234db930-16c7-41a8-94ea-ed79ba236d23",[136],[1288,1296],{"id":1289,"sortIndex":19,"affiliation":1290,"properties":18},"1a87700a-00af-43ee-ad8e-b9e493470dcb",{"id":1289,"createTime":18,"updateTime":18,"relativeEntities":1291,"slug":18,"properties":1292,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1295,"statistic":18},[],{"title":1293},{"VI":1294},"ARC Centre of Excellence for Coral Reef Studies and Comparative Genomics Centre, James Cook University, Townsville, Australia",[],{"id":1297,"sortIndex":148,"affiliation":1298,"properties":18},"e9131a67-0c18-4742-af39-c219edd9f8e2",{"id":1297,"createTime":18,"updateTime":18,"relativeEntities":1299,"slug":18,"properties":1300,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1303,"statistic":18},[],{"title":1301},{"VI":1302},"Okinawa Institute of Science and Technology, Urama, Japan",[],{"title":1305,"gsAuthor":1307},{"VI":1306},"Chuya Shinzato",{"VOID":1308},"[\"WBTVmF4AAAAJ\"]",{"id":1310,"sortIndex":148,"researcher":18,"roles":1311,"affiliations":1312,"properties":1327},"f2fbabb0-4e90-4cf2-9e0f-f1f37b64348b",[136],[1313,1319],{"id":1289,"sortIndex":19,"affiliation":1314,"properties":18},{"id":1289,"createTime":18,"updateTime":18,"relativeEntities":1315,"slug":18,"properties":1316,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1318,"statistic":18},[],{"title":1317},{"VI":1294},[],{"id":1320,"sortIndex":148,"affiliation":1321,"properties":18},"0031a899-aaef-4550-94a2-796bc584fedc",{"id":1320,"createTime":18,"updateTime":18,"relativeEntities":1322,"slug":18,"properties":1323,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1326,"statistic":18},[],{"title":1324},{"VI":1325},"Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Japan",[],{"title":1328,"gsAuthor":1330},{"VI":1329},"Akira Iguchi",{"VOID":1331},"[\"iHd4zcsAAAAJ\"]",{"id":1333,"sortIndex":179,"researcher":18,"roles":1334,"affiliations":1335,"properties":1344},"21560adb-724b-46a2-847d-1b0b42fb4230",[136],[1336],{"id":1337,"sortIndex":19,"affiliation":1338,"properties":18},"b311f7da-9b04-401d-abdd-f6396e9929d5",{"id":1337,"createTime":18,"updateTime":18,"relativeEntities":1339,"slug":18,"properties":1340,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1343,"statistic":18},[],{"title":1341},{"VI":1342},"ARC Centre for the Molecular Genetics of Development, Research School of Biological Sciences, Australian National University, Canberra, Australia",[],{"title":1345},{"VI":1346},"David C Hayward",{"id":1348,"sortIndex":50,"researcher":18,"roles":1349,"affiliations":1350,"properties":1359},"bb237a28-4087-408d-8638-d50a296683d6",[136],[1351],{"id":1352,"sortIndex":19,"affiliation":1353,"properties":18},"f661c2b9-3859-4467-a6c6-2e911b1e5ec7",{"id":1352,"createTime":18,"updateTime":18,"relativeEntities":1354,"slug":18,"properties":1355,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1358,"statistic":18},[],{"title":1356},{"VI":1357},"Faculty of Life Sciences, University of Vienna, Wien, Austria",[],{"title":1360,"gsAuthor":1362},{"VI":1361},"Ulrich Technau",{"VOID":1363},"[\"RtIvguIAAAAJ\"]",{"id":1365,"sortIndex":56,"researcher":18,"roles":1366,"affiliations":1367,"properties":1374},"c3746e19-98ca-4b4c-9bb4-f9ab42a85adb",[136],[1368],{"id":1337,"sortIndex":19,"affiliation":1369,"properties":18},{"id":1337,"createTime":18,"updateTime":18,"relativeEntities":1370,"slug":18,"properties":1371,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1373,"statistic":18},[],{"title":1372},{"VI":1342},[],{"title":1375},{"VI":1376},"Eldon E Ball",{"id":1378,"sortIndex":471,"researcher":18,"roles":1379,"affiliations":1380,"properties":1387},"cb0c2c1e-0487-4284-8d61-c58fdcac704b",[136],[1381],{"id":1289,"sortIndex":19,"affiliation":1382,"properties":18},{"id":1289,"createTime":18,"updateTime":18,"relativeEntities":1383,"slug":18,"properties":1384,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1386,"statistic":18},[],{"title":1385},{"VI":1294},[],{"title":1388},{"VI":1389},"David J Miller",{"url":1282,"publisher":1391,"properties":1410},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":1392,"slug":10,"properties":1393,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":1396,"manageAffiliations":1397,"indexDatabases":1398,"url":18,"thumbnailPath":18,"statistic":1405,"gsStatistic":18,"type":18,"analyzePriority":18},[],{"title":1394,"eissn":1395},{"EN":13},{"VOID":15},[],[],[1399],{"id":24,"indexDatabase":1400,"url":35,"indexYears":36,"academicFieldIds":18,"indexDatabaseRanking":37},{"id":26,"createTime":18,"updateTime":18,"relativeEntities":1401,"label":1402,"description":1403,"key":32,"publicationTags":1404,"standard":18},[],{"EN":29,"VI":29},{"EN":29,"VI":31},[34],{"impactFactor":19,"impactFactorByYear":1406,"i10Index":51,"i10IndexLast5Year":52,"totalPublication":53,"totalPublicationByYear":1407,"totalCitation":70,"totalCitationByYear":1408,"totalCitationPerPublication":88,"totalCitationPerPublicationByYear":1409,"hindexLast5Year":105,"hindex":105},{"2012":40,"2013":41,"2014":42,"2015":43,"2016":44,"2017":45,"2018":46,"2019":47,"2020":48,"2021":49,"2022":50},{"2005":55,"2006":56,"2007":57,"2008":58,"2009":59,"2010":60,"2011":61,"2012":62,"2013":63,"2014":64,"2015":65,"2016":66,"2017":67,"2018":68,"2019":69,"2020":62},{"2005":72,"2006":73,"2007":74,"2008":75,"2009":76,"2010":77,"2011":78,"2012":79,"2013":80,"2014":81,"2015":82,"2016":83,"2017":84,"2018":85,"2019":86,"2020":87},{"2005":90,"2006":91,"2007":92,"2008":93,"2009":94,"2010":95,"2011":96,"2012":97,"2013":98,"2014":52,"2015":99,"2016":100,"2017":101,"2018":102,"2019":103,"2020":104},{"pages":1411,"volume":1413},{"VOID":1412},"1-16",{"VOID":1414},"8",{"total":19,"publishYear":637,"statisticByYear":1416},{},"2008-11-12","2026-07-26T14:30:46.645+00:00",[37],{"id":1421,"createTime":1422,"updateTime":1423,"relativeEntities":1424,"slug":1425,"properties":1426,"entityType":127,"verifyStatus":128,"verifyTime":1441,"verifyNote":130,"languages":1442,"translateLanguages":18,"viewCount":19,"primaryUrl":1443,"fullTextUrl":18,"authors":1444,"publicationType":241,"publisherRelationship":1517,"citationCount":19,"citationInfo":1541,"publishDate":1543,"publishYear":891,"citationAnalyzeStatus":271,"lastCitationAnalyze":1544,"indexDatabases":1545,"openAccess":18,"references":1546,"isForceReanalyzing":274},"32c49e73-959a-4495-80f9-c0372d3ec15f","2024-04-17T17:52:00.033+00:00","2026-07-25T20:24:41.909+00:00",[],"Diversification-of-defensins-and-NLRs-in-Arabidopsis-species-by-different-evolutionary-mechanisms",{"mag":1427,"gsPaper":1429,"pmc":1431,"openalex":1433,"title":1435,"pm":1437,"doi":1439},{"VOID":1428},"2773279208",{"VOID":1430},"[\"14199016809545430486\"]",{"VOID":1432},"5731061",{"VOID":1434},"W2773279208",{"EN":1436},"Diversification of defensins and NLRs in Arabidopsis species by different evolutionary mechanisms",{"VOID":1438},"29246101",{"VOID":1440},"10.1186\u002Fs12862-017-1099-4","2024-05-14T09:57:52.925+00:00",[375],"https:\u002F\u002Fbmcevolbiol.biomedcentral.com\u002Farticles\u002F10.1186\u002Fs12862-017-1099-4",[1445,1464,1485,1500],{"id":1446,"sortIndex":19,"researcher":18,"roles":1447,"affiliations":1448,"properties":1457},"e3f1b578-060c-446c-85a9-4c04a86e1d6b",[],[1449],{"id":1450,"sortIndex":19,"affiliation":1451,"properties":18},"9b58966c-8349-4d52-a1dc-5393b441acc1",{"id":1450,"createTime":18,"updateTime":18,"relativeEntities":1452,"slug":18,"properties":1453,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1456,"statistic":18},[],{"title":1454},{"EN":1455},"Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätstraße 31, 93053, Regensburg, Germany",[],{"title":1458,"gsAuthor":1460,"openalex":1462},{"EN":1459},"Mariana Mondragón-Palomino",{"VOID":1461},"[\"ypgtbgYAAAAJ\"]",{"VOID":1463},"A5036855096",{"id":1465,"sortIndex":148,"researcher":18,"roles":1466,"affiliations":1467,"properties":1476},"3e3f98df-52ca-420c-8a86-a211604318a7",[],[1468],{"id":1469,"sortIndex":19,"affiliation":1470,"properties":18},"c2f6fcfe-31d8-410e-91e5-024f8d8f994f",{"id":1469,"createTime":18,"updateTime":18,"relativeEntities":1471,"slug":18,"properties":1472,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1475,"statistic":18},[],{"title":1473},{"EN":1474},"Chair of Phytopathology, Technical University of Munich, School of Life Sciences Weihenstephan, Emil-Ramann-Str. 2, 85354, Freising, Germany",[],{"orcid":1477,"title":1479,"gsAuthor":1481,"openalex":1483},{"VOID":1478},"https:\u002F\u002Forcid.org\u002F0000-0002-3444-6954",{"EN":1480},"Remco Stam",{"VOID":1482},"[\"VvswgHoAAAAJ\"]",{"VOID":1484},"A5037993228",{"id":1486,"sortIndex":179,"researcher":18,"roles":1487,"affiliations":1488,"properties":1495},"ed65f544-1c51-415c-83df-a351e9b08e4a",[],[1489],{"id":1450,"sortIndex":19,"affiliation":1490,"properties":18},{"id":1450,"createTime":18,"updateTime":18,"relativeEntities":1491,"slug":18,"properties":1492,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1494,"statistic":18},[],{"title":1493},{"EN":1455},[],{"title":1496,"openalex":1498},{"EN":1497},"Ajay John-Arputharaj",{"VOID":1499},"A5078682381",{"id":1501,"sortIndex":50,"researcher":18,"roles":1502,"affiliations":1503,"properties":1510},"7e353a79-5163-41e1-a0e6-49fc78eea29c",[],[1504],{"id":1450,"sortIndex":19,"affiliation":1505,"properties":18},{"id":1450,"createTime":18,"updateTime":18,"relativeEntities":1506,"slug":18,"properties":1507,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1509,"statistic":18},[],{"title":1508},{"EN":1455},[],{"orcid":1511,"title":1513,"openalex":1515},{"VOID":1512},"https:\u002F\u002Forcid.org\u002F0000-0001-6442-4302",{"EN":1514},"Thomas Dresselhaus",{"VOID":1516},"A5013870582",{"url":18,"publisher":1518,"properties":1537},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":1519,"slug":10,"properties":1520,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":1523,"manageAffiliations":1524,"indexDatabases":1525,"url":18,"thumbnailPath":18,"statistic":1532,"gsStatistic":18,"type":18,"analyzePriority":18},[],{"title":1521,"eissn":1522},{"EN":13},{"VOID":15},[],[],[1526],{"id":24,"indexDatabase":1527,"url":35,"indexYears":36,"academicFieldIds":18,"indexDatabaseRanking":37},{"id":26,"createTime":18,"updateTime":18,"relativeEntities":1528,"label":1529,"description":1530,"key":32,"publicationTags":1531,"standard":18},[],{"EN":29,"VI":29},{"EN":29,"VI":31},[34],{"impactFactor":19,"impactFactorByYear":1533,"i10Index":51,"i10IndexLast5Year":52,"totalPublication":53,"totalPublicationByYear":1534,"totalCitation":70,"totalCitationByYear":1535,"totalCitationPerPublication":88,"totalCitationPerPublicationByYear":1536,"hindexLast5Year":105,"hindex":105},{"2012":40,"2013":41,"2014":42,"2015":43,"2016":44,"2017":45,"2018":46,"2019":47,"2020":48,"2021":49,"2022":50},{"2005":55,"2006":56,"2007":57,"2008":58,"2009":59,"2010":60,"2011":61,"2012":62,"2013":63,"2014":64,"2015":65,"2016":66,"2017":67,"2018":68,"2019":69,"2020":62},{"2005":72,"2006":73,"2007":74,"2008":75,"2009":76,"2010":77,"2011":78,"2012":79,"2013":80,"2014":81,"2015":82,"2016":83,"2017":84,"2018":85,"2019":86,"2020":87},{"2005":90,"2006":91,"2007":92,"2008":93,"2009":94,"2010":95,"2011":96,"2012":97,"2013":98,"2014":52,"2015":99,"2016":100,"2017":101,"2018":102,"2019":103,"2020":104},{"issue":1538,"volume":1540},{"VOID":1539},"1",{"VOID":888},{"total":19,"publishYear":891,"statisticByYear":1542},{},"2017-12-01","2026-07-25T20:24:41.907+00:00",[37],[1547,1551,1555,1559,1563,1567,1571,1575,1579,1583,1587,1591,1595,1599,1603,1607,1611,1615,1619,1623,1627,1631,1635,1639,1643,1647,1651,1655,1659,1663,1667,1671,1675,1679,1683,1687,1691,1695,1699,1703,1706,1710,1714,1718,1721,1725,1729,1733,1737,1741,1745,1749,1753,1757,1761,1765,1769,1773,1777,1781,1785,1789,1793,1797,1801,1805,1809,1813,1817,1821,1825,1829,1833,1837,1840,1844,1847,1851],{"id":18,"text":1548,"url":18,"identifiers":1549},"Endo T, Ikeo K, Gojobori T. Large-scale search for genes on which positive selection may operate. Mol Biol Evol. 1996;13:685–90.",{"doi":1550},"10.1093\u002Foxfordjournals.molbev.a025629",{"id":18,"text":1552,"url":18,"identifiers":1553},"Mondragón-Palomino M, Meyers BC, Michelmore RW, Gaut BS. Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res. 2002;12:1305–15.",{"doi":1554},"10.1101\u002Fgr.159402",{"id":18,"text":1556,"url":18,"identifiers":1557},"Zhang XS, Choi JH, Heinz J, Chetty CS. Domain-specific positive selection contributes to the evolution of Arabidopsis Leucine-rich repeat receptor-like Kinase (LRR RLK) genes. J Mol Evol. 2006;63:612–21.",{"doi":1558},"10.1007\u002Fs00239-005-0187-z",{"id":18,"text":1560,"url":18,"identifiers":1561},"Bakker EG, Traw MB, Toomajian C, Kreitman M, Bergelson J. Low levels of polymorphism in genes that control the activation of defense response in Arabidopsis thaliana. Genetics. 2008;178:2031–43.",{"doi":1562},"10.1534\u002Fgenetics.107.083279",{"id":18,"text":1564,"url":18,"identifiers":1565},"Beth MM. New insights to the function of phytopathogenic bacterial type III effectors in plants. Ann Rev Plant Biol. 2005;56:509–31.",{"doi":1566},"10.1146\u002Fannurev.arplant.56.032604.144218",{"id":18,"text":1568,"url":18,"identifiers":1569},"Caldwell KS, Michelmore RW. Arabidopsis thaliana genes encoding defense signaling and recognition proteins exhibit contrasting evolutionary dynamics. Genetics. 2008;181:671–84.",{"doi":1570},"10.1534\u002Fgenetics.108.097279",{"id":18,"text":1572,"url":18,"identifiers":1573},"Bishop JG, Dean AM, Mitchell-Olds T. Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution. Proc Natl Acad Sci. 2000;97:5322–7.",{"doi":1574},"10.1073\u002Fpnas.97.10.5322",{"id":18,"text":1576,"url":18,"identifiers":1577},"Tiffin P, Hacker R, Gaut BS. Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea. Genetics. 2004;168:425–34.",{"doi":1578},"10.1534\u002Fgenetics.103.023028",{"id":18,"text":1580,"url":18,"identifiers":1581},"Bishop JG, Ripoll DR, Bashir S, Damasceno CMB, Seeds JD, Rose JKC. Selection on glycine β-1,3-endoglucanase genes differentially inhibited by a Phytophthora Glucanase inhibitor protein. Genetics. 2005;169:1009–19.",{"doi":1582},"10.1534\u002Fgenetics.103.025098",{"id":18,"text":1584,"url":18,"identifiers":1585},"Bishop JG. Directed mutagenesis confirms the functional importance of positively selected sites in Polygalacturonase inhibitor protein. Mol Biol Evol. 2005;22:1531–4.",{"doi":1586},"10.1093\u002Fmolbev\u002Fmsi146",{"id":18,"text":1588,"url":18,"identifiers":1589},"Zhao JP, Su XH. Patterns of molecular evolution and predicted function in thaumatin-like proteins of Populus trichocarpa. Planta. 2010;232:949–62.",{"doi":1590},"10.1007\u002Fs00425-010-1218-6",{"id":18,"text":1592,"url":18,"identifiers":1593},"Silverstein KAT, Moskal WA, Wu HC, Underwood BA, Graham MA, Town CD, et al. Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. Plant J. 2007;51:262–80.",{"doi":1594},"10.1111\u002Fj.1365-313X.2007.03136.x",{"id":18,"text":1596,"url":18,"identifiers":1597},"Vanoosthuyse V, Miege C, Dumas C, Cock JM. Two large Arabidopsis thaliana gene families are homologous to the Brassica gene superfamily that encodes pollen coat proteins and the male component of the self-incompatibility response. Plant Mol Biol. 2001;46:17–34.",{"doi":1598},"10.1023\u002FA:1010664704926",{"id":18,"text":1600,"url":18,"identifiers":1601},"Shenton MR, Ohyanagi H, Wang Z-X, Toyoda A, Fujiyama A, Nagata T, et al. Rapid turnover of antimicrobial-type cysteine-rich protein genes in closely related Oryza genomes. Mol Gen Genomics. 2015;290:1753–70.",{"doi":1602},"10.1007\u002Fs00438-015-1028-4",{"id":18,"text":1604,"url":18,"identifiers":1605},"Wu J, Jin X, Zhao Y, Dong Q, Jiang H, Ma Q. Evolution of the defensin-like gene family in grass genomes. J Genet. 2016;95:53–62.",{"doi":1606},"10.1007\u002Fs12041-015-0601-2",{"id":18,"text":1608,"url":18,"identifiers":1609},"Bircheneder S, Dresselhaus T. Why cellular communication during plant reproduction is particularly mediated by CRP signaling. J Exp Bot. 2016;67:4849–61.",{"doi":1610},"10.1093\u002Fjxb\u002Ferw271",{"id":18,"text":1612,"url":18,"identifiers":1613},"Franco OL. Peptide promiscuity: an evolutionary concept for plant defense. FEBS Lett. 2011;585:995–1000.",{"doi":1614},"10.1016\u002Fj.febslet.2011.03.008",{"id":18,"text":1616,"url":18,"identifiers":1617},"Schopfer CR, Nasrallah ME, Nasrallah JB. The male determinant of self-incompatibility in Brassica. Science. 1999;286:1697–700.",{"doi":1618},"10.1126\u002Fscience.286.5445.1697",{"id":18,"text":1620,"url":18,"identifiers":1621},"Takeuchi H, Higashiyama T. A species-specific cluster of defensin-like genes encodes diffusible pollen tube attractants in Arabidopsis. PLoS Biol. 2012;10:e1001449.",{"doi":1622},"10.1371\u002Fjournal.pbio.1001449",{"id":18,"text":1624,"url":18,"identifiers":1625},"Mondragón-Palomino M, John-Arputharaj A, Pallmann M, Dresselhaus T. Similarities between reproductive and immune pistil transcriptomes of Arabidopsis species. Plant Physiol. 2017;174:1559–75.",{"doi":1626},"10.1104\u002Fpp.17.00390",{"id":18,"text":1628,"url":18,"identifiers":1629},"Mee Do H, Chul Lee S, Won Jung H, Hoon Sohn K, Kook HB. Differential expression and in situ localization of a pepper defensin (CADEF1) gene in response to pathogen infection, abiotic elicitors and environmental stresses in Capsicum annuum. Plant Sci. 2004;166:1297–305.",{"doi":1630},"10.1016\u002Fj.plantsci.2004.01.008",{"id":18,"text":1632,"url":18,"identifiers":1633},"Shahzad Z, Ranwez V, Fizames C, Marquès L, Le Martret B, Alassimone J, et al. Plant Defensin type 1 protein promiscuity and expression variation within the Arabidopsis genus shed light on zinc tolerance acquisition in Arabidopsis halleri. New Phytol. 2013;200:820–33.",{"doi":1634},"10.1111\u002Fnph.12396",{"id":18,"text":1636,"url":18,"identifiers":1637},"Chen Q, Han Z, Jiang H, Tian D, Yang S. Strong positive selection drives rapid diversification of R-genes in Arabidopsis relatives. J Mol Evol. 2010;70:137–48.",{"doi":1638},"10.1007\u002Fs00239-009-9316-4",{"id":18,"text":1640,"url":18,"identifiers":1641},"Silverstein KAT. Genome organization of more than 300 defensin-like genes in Arabidopsis. Plant Physiol. 2005;138:600–10.",{"doi":1642},"10.1104\u002Fpp.105.060079",{"id":18,"text":1644,"url":18,"identifiers":1645},"Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell. 2003;15:809–34.",{"doi":1646},"10.1105\u002Ftpc.009308",{"id":18,"text":1648,"url":18,"identifiers":1649},"Zhou P, Silverstein KA, Gao L, Walton JD, Nallu S, Guhlin J, et al. Detecting small plant peptides using SPADA. BMC Bioinformatics. 2013;14:335.",{"doi":1650},"10.1186\u002F1471-2105-14-335",{"id":18,"text":1652,"url":18,"identifiers":1653},"Steuernagel B, Jupe F, Witek K, Jones JDG, Wulff BBH. NLR-parser: rapid annotation of plant NLR complements. Bioinformatics. 2015;31:1665–7.",{"doi":1654},"10.1093\u002Fbioinformatics\u002Fbtv005",{"id":18,"text":1656,"url":18,"identifiers":1657},"Woodhouse MR, Tang H, Freeling M. Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the Rosids. Plant Cell. 2011;23:4241–53.",{"doi":1658},"10.1105\u002Ftpc.111.093567",{"id":18,"text":1660,"url":18,"identifiers":1661},"Huang Q, Dresselhaus T, Gu H, Qu L-J. Active role of small peptides in Arabidopsis reproduction: expression evidence. J Integr Plant Biol. 2015;57:518–21.",{"doi":1662},"10.1111\u002Fjipb.12356",{"id":18,"text":1664,"url":18,"identifiers":1665},"Hammond-Kosack KE, Jones JDG. Resistance gene-dependent plant defense responses. Plant Cell. 1996;8:1773–91.",{"doi":1666},"10.1105\u002Ftpc.8.10.1773",{"id":18,"text":1668,"url":18,"identifiers":1669},"Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND. Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J. 1999;20:317–32.",{"doi":1670},"10.1046\u002Fj.1365-313X.1999.t01-1-00606.x",{"id":18,"text":1672,"url":18,"identifiers":1673},"Pan Q, Wendel J, Fluhr R. Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J Mol Evol. 2000;50:203–13.",{"doi":1674},"10.1007\u002Fs002399910023",{"id":18,"text":1676,"url":18,"identifiers":1677},"Mun J-H, Yu H-J, Park S, Park B-S. Genome-wide identification of NBS-encoding resistance genes in Brassica rapa. Mol Gen Genomics. 2009;282:617–31.",{"doi":1678},"10.1007\u002Fs00438-009-0492-0",{"id":18,"text":1680,"url":18,"identifiers":1681},"Li J, Ding J, Zhang W, Zhang Y, Tang P, Chen J-Q, et al. Unique evolutionary pattern of numbers of gramineous NBS–LRR genes. Mol Gen Genomics. 2010;283:427–38.",{"doi":1682},"10.1007\u002Fs00438-010-0527-6",{"id":18,"text":1684,"url":18,"identifiers":1685},"Stam R, Scheikl D, Tellier A. Pooled enrichment sequencing identifies diversity and evolutionary pressures at NLR resistance genes within a wild tomato population. Genome Biol Evol. 2016;8:1501–15.",{"doi":1686},"10.1093\u002Fgbe\u002Fevw094",{"id":18,"text":1688,"url":18,"identifiers":1689},"Vining KJ, Johnson SR, Ahkami A, Lange I, Parrish AN, Trapp SC, et al. Draft genome sequence of Mentha longifolia and development of resources for mint cultivar improvement. Mol Plant. 2017;10:323–39.",{"doi":1690},"10.1016\u002Fj.molp.2016.10.018",{"id":18,"text":1692,"url":18,"identifiers":1693},"Nishimura MT, Anderson RG, Cherkis KA, Law TF, Liu QL, Machius M, et al. TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis. Proc Natl Acad Sci. 2017;114:E2053–62.",{"doi":1694},"10.1073\u002Fpnas.1620973114",{"id":18,"text":1696,"url":18,"identifiers":1697},"Guo YL, Fitz J, Schneeberger K, Ossowski S, Cao J, Weigel D. Genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in Arabidopsis. Plant Physiol. 2011;157:757–69.",{"doi":1698},"10.1104\u002Fpp.111.181990",{"id":18,"text":1700,"url":18,"identifiers":1701},"Guo X, Liu J, Hao G, Zhang L, Mao K, Wang X, et al. Plastome phylogeny and early diversification of Brassicaceae. BMC Genomics. 2017;18:176.",{"doi":1702},"10.1186\u002Fs12864-017-3555-3",{"id":18,"text":1704,"url":18,"identifiers":1705},"Salemi M, Vandamme A-M. The phylogenetic handbook: a practical approach to DNA and protein phylogeny. Cambridge: Cambridge University Press; 2003.",{},{"id":18,"text":1707,"url":18,"identifiers":1708},"Anisimova M, Nielsen R, Yang Z. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics. 2003;164:1229–36.",{"doi":1709},"10.1093\u002Fgenetics\u002F164.3.1229",{"id":18,"text":1711,"url":18,"identifiers":1712},"Shriner D, Nickle DC, Jensen MA, Mullins JI. Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet Res. 2003;81:115–21.",{"doi":1713},"10.1017\u002FS0016672303006128",{"id":18,"text":1715,"url":18,"identifiers":1716},"Mondragon-Palomino M, Gaut BS. Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana. Mol Biol Evol. 2005;22:2444–56.",{"doi":1717},"10.1093\u002Fmolbev\u002Fmsi241",{"id":18,"text":1719,"url":18,"identifiers":1720},"Sawyer, SA. Geneconv: a computer package for the statistical detection of gene conversion 1989. Available from: http:\u002F\u002Fwww.math.wustl.edu\u002F~sawyer\u002Fgeneconv\u002F .",{},{"id":18,"text":1722,"url":18,"identifiers":1723},"Kosakovsky Pond SL. Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol. 2006;23:1891–901.",{"doi":1724},"10.1093\u002Fmolbev\u002Fmsl051",{"id":18,"text":1726,"url":18,"identifiers":1727},"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, W M, et al. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.",{"doi":1728},"10.1016\u002FS0022-2836(05)80360-2",{"id":18,"text":1730,"url":18,"identifiers":1731},"Altschul SF. A protein alignment scoring system sensitive at all evolutionary distances. J Mol Evol. 1993;36:290–300.",{"doi":1732},"10.1007\u002FBF00160485",{"id":18,"text":1734,"url":18,"identifiers":1735},"Yang Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24:1586–91.",{"doi":1736},"10.1093\u002Fmolbev\u002Fmsm088",{"id":18,"text":1738,"url":18,"identifiers":1739},"Murrell B, Moola S, Mabona A, Weighill T, Sheward D, Kosakovsky Pond SL, et al. FUBAR: a Fast, unconstrained Bayesian AppRoximation for inferring selection. Mol Biol Evol. 2013;30:1196–205.",{"doi":1740},"10.1093\u002Fmolbev\u002Fmst030",{"id":18,"text":1742,"url":18,"identifiers":1743},"Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998;8:186–94.",{"doi":1744},"10.1101\u002Fgr.8.3.186",{"id":18,"text":1746,"url":18,"identifiers":1747},"Michelmore RW, Meyers BC. Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res. 1998;8:1113–30.",{"doi":1748},"10.1101\u002Fgr.8.11.1113",{"id":18,"text":1750,"url":18,"identifiers":1751},"Takken FL, Goverse A. How to build a pathogen detector: structural basis of NB-LRR function. Curr Opin Plant Biol. 2012;15:375–84.",{"doi":1752},"10.1016\u002Fj.pbi.2012.05.001",{"id":18,"text":1754,"url":18,"identifiers":1755},"Hughes AL, Yeager M. Coordinated amino acid changes in the evolution of mammalian defensins. J Mol Evol. 1997;44:675–82.",{"doi":1756},"10.1007\u002FPL00006191",{"id":18,"text":1758,"url":18,"identifiers":1759},"Lynn DJ, Lloyd AT, Fares MA, O’Farrelly C. Evidence of positively selected sites in mammalian α-defensins. Mol Biol Evol. 2004;21:819–27.",{"doi":1760},"10.1093\u002Fmolbev\u002Fmsh084",{"id":18,"text":1762,"url":18,"identifiers":1763},"Das S, Nikolaidis N, Goto H, McCallister C, Li J, Hirano M, et al. Comparative genomics and evolution of the alpha-defensin multigene family in primates. Mol Biol Evol. 2010;27:2333–43.",{"doi":1764},"10.1093\u002Fmolbev\u002Fmsq118",{"id":18,"text":1766,"url":18,"identifiers":1767},"Chapman JR, Hellgren O, Helin AS, Kraus RHS, Cromie RL, Waldenström J. The evolution of innate immune genes: purifying and balancing selection on β-defensins in waterfowl. Mol Biol Evol. 2016;33:3075–87.",{"doi":1768},"10.1093\u002Fmolbev\u002Fmsw167",{"id":18,"text":1770,"url":18,"identifiers":1771},"Shafee TMA, Lay FT, Hulett MD, Anderson MA. The defensins consist of two independent, convergent protein superfamilies. Mol Biol Evol. 2016;33:2345–56.",{"doi":1772},"10.1093\u002Fmolbev\u002Fmsw106",{"id":18,"text":1774,"url":18,"identifiers":1775},"Schmid K, Yang Z. The trouble with sliding windows and the selective pressure in BRCA1. PLoS One. 2008;3:e3746.",{"doi":1776},"10.1371\u002Fjournal.pone.0003746",{"id":18,"text":1778,"url":18,"identifiers":1779},"Wang T, Liang L, Xue Y, Jia P-F, Chen W, Zhang M-X, et al. A receptor heteromer mediates the male perception of female attractants in plants. Nature. 2016;531:241–4.",{"doi":1780},"10.1038\u002Fnature16975",{"id":18,"text":1782,"url":18,"identifiers":1783},"Takeuchi H, Higashiyama T. Tip-localized receptors control pollen tube growth and LURE sensing in Arabidopsis. Nature. 2016;531:245–8.",{"doi":1784},"10.1038\u002Fnature17413",{"id":18,"text":1786,"url":18,"identifiers":1787},"Talke IN, Hanikenne M, Krämer U. Zinc-dependent global transcriptional control, transcriptional deregulation, and higher gene copy number for genes in metal homeostasis of the hyperaccumulator Arabidopsis Halleri. Plant Physiol. 2006;142:148–67.",{"doi":1788},"10.1104\u002Fpp.105.076232",{"id":18,"text":1790,"url":18,"identifiers":1791},"Bailey TL, Boden M, Buske F a, Frith M, Grant CE, Clementi L, et al. MEME-suite: tools for motif discovery and searching. Nucleic Acids Res. 2009;37:W202–8.",{"doi":1792},"10.1093\u002Fnar\u002Fgkp335",{"id":18,"text":1794,"url":18,"identifiers":1795},"Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.",{"doi":1796},"10.1093\u002Fmolbev\u002Fmst010",{"id":18,"text":1798,"url":18,"identifiers":1799},"Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 2010;38:W23–8.",{"doi":1800},"10.1093\u002Fnar\u002Fgkq443",{"id":18,"text":1802,"url":18,"identifiers":1803},"Sela I, Ashkenazy H, Katoh K, Pupko T. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Res. 2015;43:W7–14.",{"doi":1804},"10.1093\u002Fnar\u002Fgkv318",{"id":18,"text":1806,"url":18,"identifiers":1807},"Lefort V, Longueville J-E, Gascuel O. SMS: smart model selection in PhyML. Mol Biol Evol. 2017;34:2422–4.",{"doi":1808},"10.1093\u002Fmolbev\u002Fmsx149",{"id":18,"text":1810,"url":18,"identifiers":1811},"Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21.",{"doi":1812},"10.1093\u002Fsysbio\u002Fsyq010",{"id":18,"text":1814,"url":18,"identifiers":1815},"Xia X. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Mol Biol Evol. 2013;30:1720–8.",{"doi":1816},"10.1093\u002Fmolbev\u002Fmst064",{"id":18,"text":1818,"url":18,"identifiers":1819},"Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8:785–6.",{"doi":1820},"10.1038\u002Fnmeth.1701",{"id":18,"text":1822,"url":18,"identifiers":1823},"Matsubayashi Y. Posttranslationally modified small-peptide signals in plants. Annu Rev Plant Biol. 2014;65:385–413.",{"doi":1824},"10.1146\u002Fannurev-arplant-050312-120122",{"id":18,"text":1826,"url":18,"identifiers":1827},"Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.",{"doi":1828},"10.1093\u002Fnar\u002Fgkh340",{"id":18,"text":1830,"url":18,"identifiers":1831},"Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010;27:221–4.",{"doi":1832},"10.1093\u002Fmolbev\u002Fmsp259",{"id":18,"text":1834,"url":18,"identifiers":1835},"Liu W, Xie Y, Ma J, Luo X, Nie P, Zuo Z, et al. IBS: an illustrator for the presentation and visualization of biological sequences. Bioinformatics. 2015;31:3359–61.",{"doi":1836},"10.1093\u002Fbioinformatics\u002Fbtv362",{"id":18,"text":1838,"url":18,"identifiers":1839},"Linkmeyer AMH. Fusarium head blight of barley: epidemiology and host-pathogen interaction Technische Universität München; 2012.",{},{"id":18,"text":1841,"url":18,"identifiers":1842},"Hoefle C, Huesmann C, Schultheiss H, Börnke F, Hensel G, Kumlehn J, et al. A barley ROP GTPase activating protein associates with microtubules and regulates entry of the barley powdery mildew fungus into leaf epidermal cells. Plant Cell. 2011;23:2422–39.",{"doi":1843},"10.1105\u002Ftpc.110.082131",{"id":18,"text":1845,"url":18,"identifiers":1846},"Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. Available from: http:\u002F\u002Fwww.bioinformatics.babraham.ac.uk\u002Fprojects\u002Ffastqc .",{},{"id":18,"text":1848,"url":18,"identifiers":1849},"Rawat V, Abdelsamad A, Pietzenuk B, Seymour DK, Koenig D, Weigel D, et al. Improving the annotation of Arabidopsis lyrata using RNA-Seq data. PLoS One. 2015;10:e0137391. Provart NJ, editor",{"doi":1850},"10.1371\u002Fjournal.pone.0137391",{"id":18,"text":1852,"url":18,"identifiers":1853},"Robinson MD, McCarthy DJ, Smyth GK. EdgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.",{"doi":1854},"10.1093\u002Fbioinformatics\u002Fbtp616",{"id":1856,"createTime":1857,"updateTime":1858,"relativeEntities":1859,"slug":1860,"properties":1861,"entityType":127,"verifyStatus":128,"verifyTime":1872,"verifyNote":130,"languages":18,"translateLanguages":18,"viewCount":19,"primaryUrl":1873,"fullTextUrl":18,"authors":1874,"publicationType":241,"publisherRelationship":1892,"citationCount":18,"citationInfo":18,"publishDate":1916,"publishYear":706,"citationAnalyzeStatus":17,"lastCitationAnalyze":1858,"indexDatabases":1917,"openAccess":18,"references":18,"isForceReanalyzing":274},"9af60af9-1396-420a-8158-87ccfaa6ed4c","2023-11-30T03:53:35.847+00:00","2026-07-23T16:48:52.926+00:00",[],"Sleeping-to-fuel-the-immune-system-mammalian-sleep-and-resistance-to-parasites",{"abstract":1862,"title":1864,"gsPaper":1866,"references":1868,"doi":1870},{"EN":1863},"Sleep is an enigma. Why animals forgo eating and reproducing, while potentially increasing their risk of predation remains unknown. Although some may question whether all animals sleep, it is clear that all living organisms possess defenses against attack by pathogens. Immune responses of humans and animals are impaired by sleep loss, and responses to immune challenge include altered sleep. Thus, sleep is hypothesized to be a component of the acute phase response to infection and to function in host defense. Examining phylogenetic relationships among sleep parameters, components of the mammalian immune system and resistance to infection may provide insight into the evolution of sleep and lead to a greater appreciation for the role of sleep in host defense.",{"EN":1865},"Sleeping to fuel the immune system: mammalian sleep and resistance to parasites",{"VOID":1867},"[\"2950930308526752686\"]",{"VOID":1869},"Zimmerman JE, Naidoo N, Raizen DM, Pack AI: Conservation of sleep: insights from non-mammalian model systems. Trends Neurosci. 2008, 31: 371-376.\nCapellini I, Barton RA, McNamara P, Preston BT, Nunn CL: Phylogenetic analysis of the ecology and evolution of mammalian sleep. Evolution. 2008, 62: 1764-1776.\nAllada R, Siegel JM: Unearthing the phylogenetic roots of sleep. Curr Biol. 2008, 18: R670-R679.\nTononi G, Cirelli C: Sleep function and synaptic homeostasis. Sleep Med Rev. 2006, 10: 49-62.\nKrueger JM: A neuronal group theory of sleep function. J Sleep Res. 1993, 2: 63-69.\nLoker ES, Adema CM, Zhang SM, Kepler TB: Invertebrate immune systems – not homogeneous, not simple, not well understood. Immunol Rev. 2004, 198: 10-24.\nOpp MR: Cytokines and sleep. Sleep Med Rev. 2005, 9: 355-364.\nObal F, Krueger JM: Biochemical regulation of non-rapid-eye-movement sleep. Front Biosci. 2003, 8: d520-d550.\nKrueger JM, Majde JA: Sleep as a host defense: its regulation by microbial products and cytokines. Clin Immunol Immunopathol. 1990, 57: 188-199.\nToth LA, Tolley EA, Krueger JM: Sleep as a prognostic indicator during infectious disease in rabbits. Proc Soc Exp Biol Med. 1993, 203: 179-192.\nPreston BT, Capellini I, McNamara P, Barton RA, Nunn CL: Parasite resistance and the adaptive significance of sleep. BMC Evolutionay Biology. 2009, 9: 7-\nZhou P, Li E, Zhu N, Robertson J, Nash T, Singer SM: Role of interleukin-6 in the control of acute and chronic Giardia lamblia infections in mice. Infect Immun. 2003, 71: 1566-1568.\nZhou P, Li E, Shea-Donohue T, Singer SM: Tumour necrosis factor alpha contributes to protection against Giardia lamblia infection in mice. Parasite Immunol. 2007, 29: 367-374.\nBienz M, Dai WJ, Welle M, Gottstein B, Muller N: Interleukin-6-deficient mice are highly susceptible to Giardia lamblia infection but exhibit normal intestinal immunoglobulin A responses against the parasite. Infect Immun. 2003, 71: 1569-1573.\nOttaviani E, Franchini A, Franceschi C: Pro-opiomelanocortin-derived peptides, cytokines, and nitric oxide in immune responses and stress: an evolutionary approach. Int Rev Cytol. 1997, 170: 79-141.\nPaemen LR, Porchet-Hennere E, Masson M, Leung MK, Hughes TK, Stefano GB: Glial localization of interleukin-1 alpha in invertebrate ganglia. Cell Mol Neurobiol. 1992, 12: 463-472.\nSonetti D, Ottaviani E, Bianchi F, Rodriguez M, Stefano ML, Scharrer B, et al: Microglia in invertebrate ganglia. Proc Natl Acad Sci USA. 1994, 91: 9180-9184.\nStefano GB, Smith EM, Hughes TK: Opioid induction of immunoreactive interleukin-1 in Mytilus edulis and human immunocytes: an interleukin-1-like substance in invertebrate neural tissue. J Neuroimmunol. 1991, 32: 29-34.\nRaizen DM, Zimmerman JE, Maycock MH, Ta UD, You YJ, Sundaram MV, et al: Lethargus is a Caenorhabditis elegans sleep-like state. Nature. 2008, 451: 569-572.\nHendricks JC, Finn SM, Panckeri KA, Chavkin J, Williams JA, Sehgal A, et al: Rest in Drosophila is a sleep-like state. Neuron. 2000, 25: 129-138.\nShaw PJ, Cirelli C, Greenspan RJ, Tononi G: Correlates of sleep and waking in Drosophila melanogaster. Science. 2000, 287: 1834-1837.\nSehgal A, Joiner W, Crocker A, Koh K, Sathyanarayanan S, Fang Y, et al: Molecular Analysis of Sleep: Wake Cycles in Drosophila. Cold Spring Harb Symp Quant Biol. 2007, 72: 557-564.\nCirelli C, Bushey D: Sleep and wakefulness in Drosophila melanogaster. Ann N Y Acad Sci. 2008, 1129: 323-329.\nWilliams JA, Sathyanarayanan S, Hendricks JC, Sehgal A: Interaction between sleep and the immune response in Drosophila: a role for the NFkappaB relish. Sleep. 2007, 30: 389-400.\nShibata M, Blatteis CM: Differential effects of cytokines on thermosensitive neurons in guinea pig preoptic area slices. Am J Physiol. 1991, 261: R1096-R1103.\nKenney MJ, Blecha F, Fels RJ, Morgan DA: Altered frequency responses of sympathetic nerve discharge bursts after IL-1beta and mild hypothermia. J Appl Physiol. 2002, 93: 280-288.\nVasilenko VY, Petruchuk TA, Gourine VN, Pierau FK: Interleukin-1beta reduces temperature sensitivity but elevates thermal thresholds in different populations of warm-sensitive hypothalamic neurons in rat brain slices. Neurosci Lett. 2000, 292: 207-210.\nAlam MN, McGinty D, Bashir T, kumar S, Imeri L, Opp MR, et al: Interleukin-1β modulates state-dependent discharge activity of preoptic area and basal forebrain neurons: role in sleep regulation. Eur J Neurosci. 2004, 20: 207-216.\nBrambilla D, Franciosi S, Opp MR, Imeri L: Interleukin-1 inhibits firing of serotonergic neurons in the dorsal raphe nucleus and enhances GABAergic inhibitory post-synaptic potentials. Eur J Neurosci. 2007, 26: 1862-1869.\nDe A, Churchill L, Obal F, Simasko SM, Krueger JM: GHRH and IL1beta increase cytoplasmic Ca(2+) levels in cultured hypothalamic GABAergic neurons. Brain Res. 2002, 949: 209-212.\nDe A, Krueger JM, Simasko SM: Tumor necrosis factor alpha increases cytosolic calcium responses to AMPA and KCl in primary cultures of rat hippocampal neurons. Brain Res. 2003, 981: 133-142.\nManfridi A, Brambilla D, Bianchi S, Mariotti M, Opp MR, Imeri L: Interleukin-1β enhances non-rapid eye movement sleep when microinjected into the dorsal raphe nucleus and inhibits serotonergic neurons in vitro. Eur J Neurosci. 2003, 18: 1041-1049.\nMimura Y, Gotow T, Nishi T, Osame M: Mechanisms of hyperpolarization induced by two cytokines, hTNF alpha and hIL-1 alpha in neurons of the mollusc, Onchidium. Brain Res. 1994, 653: 112-118.\nFarr M, Mathews J, Zhu DF, Ambron RT: Inflammation causes a long-term hyperexcitability in the nociceptive sensory neurons of Aplysia. Learn Mem. 1999, 6: 331-340.",{"VOID":1871},"10.1186\u002F1471-2148-9-8","2024-06-25T00:26:47.113+00:00","http:\u002F\u002Fbmcevolbiol.biomedcentral.com\u002Farticles\u002F10.1186\u002F1471-2148-9-8",[1875],{"id":1876,"sortIndex":19,"researcher":18,"roles":1877,"affiliations":1878,"properties":1887},"003488db-d810-4c84-b28a-8ff26560cc45",[136],[1879],{"id":1880,"sortIndex":19,"affiliation":1881,"properties":18},"6c3159d2-7e8e-4108-a46f-f9affe83edd3",{"id":1880,"createTime":18,"updateTime":18,"relativeEntities":1882,"slug":18,"properties":1883,"entityType":18,"verifyStatus":18,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":18,"url":18,"parentIds":1886,"statistic":18},[],{"title":1884},{"VI":1885},"Departments of Anesthesiology and Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, USA",[],{"title":1888,"gsAuthor":1890},{"VI":1889},"Mark R Opp",{"VOID":1891},"[\"J4vCOq4AAAAJ\"]",{"url":1873,"publisher":1893,"properties":1912},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":1894,"slug":10,"properties":1895,"entityType":16,"verifyStatus":17,"verifyTime":18,"verifyNote":18,"languages":18,"translateLanguages":18,"viewCount":19,"subjectFields":1898,"manageAffiliations":1899,"indexDatabases":1900,"url":18,"thumbnailPath":18,"statistic":1907,"gsStatistic":18,"type":18,"analyzePriority":18},[],{"title":1896,"eissn":1897},{"EN":13},{"VOID":15},[],[],[1901],{"id":24,"indexDatabase":1902,"url":35,"indexYears":36,"academicFieldIds":18,"indexDatabaseRanking":37},{"id":26,"createTime":18,"updateTime":18,"relativeEntities":1903,"label":1904,"description":1905,"key":32,"publicationTags":1906,"standard":18},[],{"EN":29,"VI":29},{"EN":29,"VI":31},[34],{"impactFactor":19,"impactFactorByYear":1908,"i10Index":51,"i10IndexLast5Year":52,"totalPublication":53,"totalPublicationByYear":1909,"totalCitation":70,"totalCitationByYear":1910,"totalCitationPerPublication":88,"totalCitationPerPublicationByYear":1911,"hindexLast5Year":105,"hindex":105},{"2012":40,"2013":41,"2014":42,"2015":43,"2016":44,"2017":45,"2018":46,"2019":47,"2020":48,"2021":49,"2022":50},{"2005":55,"2006":56,"2007":57,"2008":58,"2009":59,"2010":60,"2011":61,"2012":62,"2013":63,"2014":64,"2015":65,"2016":66,"2017":67,"2018":68,"2019":69,"2020":62},{"2005":72,"2006":73,"2007":74,"2008":75,"2009":76,"2010":77,"2011":78,"2012":79,"2013":80,"2014":81,"2015":82,"2016":83,"2017":84,"2018":85,"2019":86,"2020":87},{"2005":90,"2006":91,"2007":92,"2008":93,"2009":94,"2010":95,"2011":96,"2012":97,"2013":98,"2014":52,"2015":99,"2016":100,"2017":101,"2018":102,"2019":103,"2020":104},{"pages":1913,"volume":1915},{"VOID":1914},"1-3",{"VOID":704},"2009-01-09",[37]]