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Guo L, Qiao X, Haji D, Zhou T, Liu Z, Whiteman NK, Huang J. Convergent resistance to GABA receptor neurotoxins through plant-insect coevolution. Nat Ecol Evol 2023; 7:1444-1456. [PMID: 37460839 PMCID: PMC10482695 DOI: 10.1038/s41559-023-02127-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/22/2023] [Indexed: 09/08/2023]
Abstract
The molecular mechanisms of coevolution between plants and insects remain elusive. GABA receptors are targets of many neurotoxic terpenoids, which represent the most diverse array of natural products known. Over deep evolutionary time, as plant terpene synthases diversified in plants, so did plant terpenoid defence repertoires. Here we show that herbivorous insects and their predators evolved convergent amino acid changing substitutions in duplicated copies of the Resistance to dieldrin (Rdl) gene that encodes the GABA receptor, and that the evolution of duplicated Rdl and terpenoid-resistant GABA receptors is associated with the diversification of moths and butterflies. These same substitutions also evolved in pests exposed to synthetic insecticides that target the GABA receptor. We used in vivo genome editing in Drosophila melanogaster to evaluate the fitness effects of each putative resistance mutation and found that pleiotropy both facilitates and constrains the evolution of GABA receptor resistance. The same genetic changes that confer resistance to terpenoids across 300 Myr of insect evolution have re-evolved in response to synthetic analogues over one human lifespan.
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Affiliation(s)
- Lei Guo
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | | | - Diler Haji
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Tianhao Zhou
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhihan Liu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Noah K Whiteman
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
| | - Jia Huang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.
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2
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Peláez JN, Gloss AD, Ray JF, Chaturvedi S, Haji D, Charboneau JLM, Verster KI, Whiteman NK. Evolution and genomic basis of the plant-penetrating ovipositor: a key morphological trait in herbivorous Drosophilidae. Proc Biol Sci 2022; 289:20221938. [PMID: 36350206 PMCID: PMC9653217 DOI: 10.1098/rspb.2022.1938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Herbivorous insects are extraordinarily diverse, yet are found in only one-third of insect orders. This skew may result from barriers to plant colonization, coupled with phylogenetic constraint on plant-colonizing adaptations. The plant-penetrating ovipositor, however, is one trait that surmounts host plant physical defences and may be evolutionarily labile. Ovipositors densely lined with hard bristles have evolved repeatedly in herbivorous lineages, including within the Drosophilidae. However, the evolution and genetic basis of this innovation has not been well studied. Here, we focused on the evolution of this trait in Scaptomyza, a genus sister to Hawaiian Drosophila, that contains a herbivorous clade. Our phylogenetic approach revealed that ovipositor bristle number increased as herbivory evolved in the Scaptomyza lineage. Through a genome-wide association study, we then dissected the genomic architecture of variation in ovipositor bristle number within S. flava. Top-associated variants were enriched for transcriptional repressors, and the strongest associations included genes contributing to peripheral nervous system development. Individual genotyping supported the association at a variant upstream of Gαi, a neural development gene, contributing to a gain of 0.58 bristles/major allele. These results suggest that regulatory variation involving conserved developmental genes contributes to this key morphological trait involved in plant colonization.
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Affiliation(s)
- Julianne N. Peláez
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | - Andrew D. Gloss
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10012, USA,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Julianne F. Ray
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Samridhi Chaturvedi
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | - Diler Haji
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | | | - Kirsten I. Verster
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | - Noah K. Whiteman
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA,Department of Molecular and Cell Biology, University of California, Berkeley, 94720 CA, USA
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3
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Alexandre NM, Haji D, Bakhtiari M, Chatla K, Aguilar JM, Arzumanova K, Whiteman NK. A Reference Genome Assembly of Hybrid-Derived California Wild Radish (Raphanus sativus × raphanistrum). J Hered 2022; 113:197-204. [PMID: 35575080 PMCID: PMC9113464 DOI: 10.1093/jhered/esab076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/24/2021] [Indexed: 01/30/2023] Open
Abstract
For agriculturally important plants, pollination and herbivory are 2 ecological factors that play into the success of crop yields. Each is also important in natural environments where invasive plants and their effect on species interactions may alter the native ecology. The California Wild Radish (Raphanus sativus × raphanistrum), a hybrid derived from an agriculturally important crop and a nonnative cultivar, is common in California. Remarkably, it has recently replaced wild populations of both progenitor species. Experiments on phenotypic variation for petal color and antiherbivore defenses suggest both pairs of polymorphisms are maintained as a result of pollinator- and herbivore-mediated natural selection. This species provides an opportunity to understand how natural selection shapes the evolution of ecologically important traits when traits are constrained by 2 opposing forces. Here we provide the genome assembly of the California Wild Radish displaying improvement to currently existing genomes for agronomically important crucifers. This genome sequence provides the tools to dissect the genomic architecture of traits related to herbivory and pollination using natural variation in the wild as well as the ability to infer demographic and selective history in the context of hybridization. Study systems like these will improve our understanding and predictions of evolutionary change for correlated traits.
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Affiliation(s)
- Nicolas M Alexandre
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Diler Haji
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Moe Bakhtiari
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jessica M Aguilar
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ksenia Arzumanova
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Noah K Whiteman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
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4
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Kim BY, Wang JR, Miller DE, Barmina O, Delaney E, Thompson A, Comeault AA, Peede D, D'Agostino ERR, Pelaez J, Aguilar JM, Haji D, Matsunaga T, Armstrong E, Zych M, Ogawa Y, Stamenković-Radak M, Jelić M, Veselinović MS, Tanasković M, Erić P, Gao JJ, Katoh TK, Toda MJ, Watabe H, Watada M, Davis JS, Moyle LC, Manoli G, Bertolini E, Košťál V, Hawley RS, Takahashi A, Jones CD, Price DK, Whiteman N, Kopp A, Matute DR, Petrov DA. Correction: Highly contiguous assemblies of 101 drosophilid genomes. eLife 2022; 11:e78579. [PMID: 35302486 PMCID: PMC8933002 DOI: 10.7554/elife.78579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
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Kim BY, Wang JR, Miller DE, Barmina O, Delaney E, Thompson A, Comeault AA, Peede D, D'Agostino ERR, Pelaez J, Aguilar JM, Haji D, Matsunaga T, Armstrong EE, Zych M, Ogawa Y, Stamenković-Radak M, Jelić M, Veselinović MS, Tanasković M, Erić P, Gao JJ, Katoh TK, Toda MJ, Watabe H, Watada M, Davis JS, Moyle LC, Manoli G, Bertolini E, Košťál V, Hawley RS, Takahashi A, Jones CD, Price DK, Whiteman N, Kopp A, Matute DR, Petrov DA. Highly contiguous assemblies of 101 drosophilid genomes. eLife 2021; 10:e66405. [PMID: 34279216 PMCID: PMC8337076 DOI: 10.7554/elife.66405] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022] Open
Abstract
Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.
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Affiliation(s)
- Bernard Y Kim
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Jeremy R Wang
- Department of Genetics, University of North CarolinaChapel HillUnited States
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s HospitalSeattleUnited States
| | - Olga Barmina
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Emily Delaney
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Ammon Thompson
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Aaron A Comeault
- School of Natural Sciences, Bangor UniversityBangorUnited Kingdom
| | - David Peede
- Biology Department, University of North CarolinaChapel HillUnited States
| | | | - Julianne Pelaez
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Jessica M Aguilar
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Diler Haji
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Teruyuki Matsunaga
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | | | - Molly Zych
- Molecular and Cellular Biology Program, University of WashingtonSeattleUnited States
| | - Yoshitaka Ogawa
- Department of Biological Sciences, Tokyo Metropolitan UniversityHachiojiJapan
| | | | - Mihailo Jelić
- Faculty of Biology, University of BelgradeBelgradeSerbia
| | | | - Marija Tanasković
- University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of SerbiaBelgradeSerbia
| | - Pavle Erić
- University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of SerbiaBelgradeSerbia
| | - Jian-Jun Gao
- School of Ecology and Environmental Science, Yunnan UniversityKunmingChina
| | - Takehiro K Katoh
- School of Ecology and Environmental Science, Yunnan UniversityKunmingChina
| | | | - Hideaki Watabe
- Biological Laboratory, Sapporo College, Hokkaido University of EducationSapporoJapan
| | - Masayoshi Watada
- Graduate School of Science and Engineering, Ehime UniversityMatsuyamaJapan
| | - Jeremy S Davis
- Department of Biology, University of KentuckyLexingtonUnited States
| | - Leonie C Moyle
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Giulia Manoli
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of WürzburgWürzburgGermany
| | - Enrico Bertolini
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of WürzburgWürzburgGermany
| | - Vladimír Košťál
- Institute of Entomology, Biology Centre, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - R Scott Hawley
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Stowers Institute for Medical ResearchKansas CityUnited States
| | - Aya Takahashi
- Department of Biological Sciences, Tokyo Metropolitan UniversityHachiojiJapan
| | - Corbin D Jones
- Biology Department, University of North CarolinaChapel HillUnited States
| | - Donald K Price
- School of Life Science, University of NevadaLas VegasUnited States
| | - Noah Whiteman
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Daniel R Matute
- Biology Department, University of North CarolinaChapel HillUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
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6
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Simon C, Gordon ERL, Moulds MS, Cole JA, Haji D, Lemmon AR, Lemmon EM, Kortyna M, Nazario K, Wade EJ, Meister RC, Goemans G, Chiswell SM, Pessacq P, Veloso C, McCutcheon JP, Łukasik P. Corrigendum: Off-target capture data, endosymbiont genes and morphology reveal a relict lineage that is sister to all other singing cicadas. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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7
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Simon C, Gordon ERL, Moulds MS, Cole JA, Haji D, Lemmon AR, Lemmon EM, Kortyna M, Nazario K, Wade EJ, Meister RC, Goemans G, Chiswell SM, Pessacq P, Veloso C, McCutcheon JP, Łukasik P. Off-target capture data, endosymbiont genes and morphology reveal a relict lineage that is sister to all other singing cicadas. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Phylogenetic asymmetry is common throughout the tree of life and results from contrasting patterns of speciation and extinction in the paired descendant lineages of ancestral nodes. On the depauperate side of a node, we find extant ‘relict’ taxa that sit atop long, unbranched lineages. Here, we show that a tiny, pale green, inconspicuous and poorly known cicada in the genus Derotettix, endemic to degraded salt-plain habitats in arid regions of central Argentina, is a relict lineage that is sister to all other modern cicadas. Nuclear and mitochondrial phylogenies of cicadas inferred from probe-based genomic hybrid capture data of both target and non-target loci and a morphological cladogram support this hypothesis. We strengthen this conclusion with genomic data from one of the cicada nutritional bacterial endosymbionts, Sulcia, an ancient and obligate endosymbiont of the larger plant-sucking bugs (Auchenorrhyncha) and an important source of maternally inherited phylogenetic data. We establish Derotettiginae subfam. nov. as a new, monogeneric, fifth cicada subfamily, and compile existing and new data on the distribution, ecology and diet of Derotettix. Our consideration of the palaeoenvironmental literature and host-plant phylogenetics allows us to predict what might have led to the relict status of Derotettix over 100 Myr of habitat change in South America.
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Affiliation(s)
- Chris Simon
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Eric R L Gordon
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - M S Moulds
- Australian Museum Research Institute, Sydney, NSW, Australia
| | - Jeffrey A Cole
- Natural Sciences Division, Pasadena City College, Pasadena, CA, USA
| | - Diler Haji
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | | | - Michelle Kortyna
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Katherine Nazario
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Elizabeth J Wade
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Department of Natural Sciences and Mathematics, Curry College, Milton, MA, USA
| | - Russell C Meister
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Geert Goemans
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | | | - Pablo Pessacq
- Centro de Investigaciones Esquel de Montaña y Estepa Patagónicas, Esquel, Chubut, Argentina
| | - Claudio Veloso
- Department of Ecological Sciences, Science Faculty, University of Chile, Santiago, Chile
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Piotr Łukasik
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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Cooley JR, Arguedas N, Bonaros E, Bunker G, Chiswell SM, DeGiovine A, Edwards M, Hassanieh D, Haji D, Knox J, Kritsky G, Mills C, Mozgai D, Troutman R, Zyla J, Hasegawa H, Sota T, Yoshimura J, Simon C. The periodical cicada four-year acceleration hypothesis revisited and the polyphyletic nature of Brood V, including an updated crowd-source enhanced map (Hemiptera: Cicadidae: Magicicada). PeerJ 2018; 6:e5282. [PMID: 30083444 PMCID: PMC6074776 DOI: 10.7717/peerj.5282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 06/26/2018] [Indexed: 11/20/2022] Open
Abstract
The periodical cicadas of North America (Magicicada spp.) are well-known for their long life cycles of 13 and 17 years and their mass synchronized emergences. Although periodical cicada life cycles are relatively strict, the biogeographic patterns of periodical cicada broods, or year-classes, indicate that they must undergo some degree of life cycle switching. We present a new map of periodical cicada Brood V, which emerged in 2016, and demonstrate that it consists of at least four distinct parts that span an area in the United States stretching from Ohio to Long Island. We discuss mtDNA haplotype variation in this brood in relation to other periodical cicada broods, noting that different parts of this brood appear to have different origins. We use this information to refine a hypothesis for the formation of periodical cicada broods by 1- and 4-year life cycle jumps.
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Affiliation(s)
- John R Cooley
- College of Integrative Sciences, Wesleyan University, Middletown, CT, United States of America.,Department of Ecology and Evolutionary Biology, The University of Connecticut, Storrs, CT, United States of America
| | - Nidia Arguedas
- Cleveland Metroparks, Cleveland, OH, United States of America
| | | | - Gerry Bunker
- Massachusetts Cicadas, Marlborough, MA, United States of America
| | - Stephen M Chiswell
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | | | - Marten Edwards
- Department of Biology, Muhlenberg College, Allentown, PA, United States of America
| | - Diane Hassanieh
- Department of Ecology and Evolutionary Biology, The University of Connecticut, Storrs, CT, United States of America
| | - Diler Haji
- Department of Ecology and Evolutionary Biology, The University of Connecticut, Storrs, CT, United States of America
| | - John Knox
- Department of Biology, Washington and Lee University, Lexington, VA, United States of America
| | - Gene Kritsky
- Department of Biology, Mount St. Joseph University, Cincinnati, OH, United States of America
| | - Carolyn Mills
- Research Services, The University of Connecticut Libraries, Storrs, CT, United States of America
| | - Dan Mozgai
- Cicada mania, NJ, United States of America
| | | | - John Zyla
- Mid-Atlantic Cicadas, MD, United States of America
| | - Hiroki Hasegawa
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Jin Yoshimura
- Graduate School of Science and Technology, Shizuoka University, Hamamatsu, Japan
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, The University of Connecticut, Storrs, CT, United States of America
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Haji K, Haji D, Le Blanc V, Botha J. Effect of prolonged emergency department length of stay on inpatient length of stay and inhospital mortality in severe sepsis and septic shock. Crit Care 2008. [PMCID: PMC4088789 DOI: 10.1186/cc6639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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