The Scirtothrips dorsalis species complex: Endemism and invasion in a global pest

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Dickey, Aaron M ^a,b,e   Kumar, Vivek ^a,b   Hoddle, Mark S ^c   Funderburk, Joe E ^d   Morgan, J Kent ^b,f   Jara Cavieres, Antonella ^a,b   Shatters, Robert G ^b   Osborne, Lance S ^a   McKenzie, Cindy L ^b  

^a UNIVERSITY OF FLORIDA   (United States)

^b U S HORTICULTURAL RESEARCH LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF FLORIDA   (United States)

^e AGRICULTURAL RESEARCH SERVICE   (United States)

^f J Kent Morgan Consulting   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; CYTOCHROME C OXIDASE I; GENOMIC DNA; UNCLASSIFIED DRUG;

ARTICLE; CODON; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; DNA BARCODING; GENE AMPLIFICATION; GENE LOCUS; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC VARIABILITY; HAPLOTYPE; HISTOGRAM; INTRON; MORPHOLOGY; NEXT GENERATION SEQUENCING; NONHUMAN; PARASITE TRANSMISSION; PHYLOGENY; PHYLOGEOGRAPHY; PLANT PEST; POLYMERASE CHAIN REACTION; POPULATION GENETICS; RESTRICTION FRAGMENT; SCIRTOTHRIPS DORSALIS; SEQUENCE HOMOLOGY; SPECIES ENDEMICITY; SPECIES IDENTIFICATION; SPECIES INVASION; TOSPOVIRUS; ANIMAL; BAYES THEOREM; DNA SEQUENCE; GENETIC VARIATION; GENETICS; INTERNATIONAL COOPERATION; INTRODUCED SPECIES; SPECIES DIFFERENCE; THYSANOPTERA;

ARTHROPODA; BACTROCERA DORSALIS SPECIES COMPLEX; SCIRTOTHRIPS DORSALIS; TOSPOVIRUS;

ANIMALS; BAYES THEOREM; ELECTRON TRANSPORT COMPLEX IV; GENETIC LOCI; GENETIC VARIATION; GENETICS, POPULATION; INTERNATIONALITY; INTRODUCED SPECIES; PHYLOGENY; PHYLOGEOGRAPHY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; THYSANOPTERA;

EID: 84928473862     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0123747     Document Type: Article

References (86)

1. Morse JG, Hoddle MS. Invasion biology of thrips. Annu Rev Entomol. 2006; 51: 67-89. PMID: 16332204
2. CABI. Scirtothrips dorsalis. In: Invasive Species Compendium. Wallingford, UK: CAB International; 2013. www.cabi.org/isc.
3. Kumar V, Kakkar G, McKenzie CL, Seal DR, Osborne LS. An overview of Chilli Thrips, Scirtothrips dorsalis (Thysanoptera: Thripidae) biology, distribution and management. In: Soloneski S, Larramendy M, editors. Weed and Pest Control: Conventional and New Challenges. InTech; 2013. doi: 10.5772/55045
4. Seal DR, Ciomperlik M, Richards ML, Klassen W. Comparative effectiveness of chemical insecticides against the chilli thrips Scirtothrips dorsalis Hood (Thysanoptera: Thripidae), on pepper and their compatibility with natural enemies. Crop Prot. 2006; 25: 949-955.
5. Mound L, Palmer J. Identification, distribution and host-plants of the pest species of Scirtothrips (Thysanoptera: Thripidae). Bull Entomol Res. 1981; 71: 467-479.
6. Gilbert M. First African record of Scirtothrips dorsalis Hood (Thysanoptera: Thripidae) a potential pest of citrus and other crops in southern Africa. J Entomol Soc South Afr. 1986; 49: 159-161.
7. Hoddle MS, Heraty JM, Rugman-Jones PF, Mound LA, Stouthamer R. Relationships among species of Scirtothrips (Thysanoptera: Thripidae, Thripinae) Using Molecular and Morphological Data. Ann Entomol Soc Am. 2008; 101: 491-500.
8. Rugman-Jones PF, Hoddle MS, Mound LA, Stouthamer R. Molecular identification key for pest species of Scirtothrips (Thysanoptera: Thripidae). J Econ Entomol. 2006; 99: 1813-1819. PMID: 17066817
9. Toda S, Komazaki S. Identification of thrips species (Thysanoptera: Thripidae) on Japanese fruit trees by polymerase chain reaction and restriction fragment length polymorphism of the ribosomal ITS2 region. Bull Entomol Res. 2002; 92: 359-363. PMID: 12191445
10. Toda S, Hirose T, Kakiuchi K, Kodama H, Kijima K, Mochizuki M. Occurrence of a novel strain of Scirtothrips dorsalis (Thysanoptera: Thripidae) in Japan and development of its molecular diagnostics. Appl Entomol Zool. 2014; 49: 231-239.
11. Rebijith K, Asokan R, Kumar NK, Krishna V, Ramamurthy V. Development of species-specific markers and molecular differences in mtDNA of Thrips palmi Karny and Scirtothrips dorsalis Hood (Thripidae: Thysanoptera), vectors of tospoviruses (Bunyaviridae) in India. Entomol News. 2012; 122: 201-213.
12. Farris R, Ruiz-Arce R, Ciomperlik M, Vasquez J, DeLeon R. Development of a ribosomal DNA ITS2 marker for the identification of the thrips, Scirtothrips dorsalis. J Insect Sci. 2010; 10: 1-15. doi: 10.1673/031.010.0101 PMID: 20569122
13. Kadirvel P, Srinivasan R, Hsu Y-C, Su F-C, Pena RDL. Application of cytochrome oxidase I sequences for phylogenetic analysis and identification of thrips species occurring on vegetable crops. J Econ Entomol. 2012; 106: 408-418.
14. Lombaert E, Guillemaud T, Thomas CE, Handley LJL, Li J, Wang S, et al. Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: a case study of the invasive ladybird Harmonia axyridis. Mol Ecol. 2011; 20: 4654-4670. doi: 10.1111/j.1365-294X.2011.05322.x PMID: 22004292
15. Foighil DÓ, Gaffney PM, Wilbur AE, Hilbish TJ. Mitochondrial cytochrome oxidase I gene sequences support an Asian origin for the Portuguese oyster Crassostrea angulata. Mar Biol. 1998; 131: 497-503.
16. Cognato AI, Sun J, Anducho-Reyes MA, Owen DR. Genetic variation and origin of red turpentine beetle (Dendroctonus valens LeConte) introduced to the People's Republic of China. Agric Forest Entomol. 2005; 7: 87-94.
17. Smith MA, Wood DM, Janzen DH, Hallwachs W, Hebert PDN. DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all generalists. Proc Natl Acad Sci USA. 2007; 104: 4967-4972. PMID: 17360352
18. Hebert PD, Penton EH, Burns JM, Janzen DH, Hallwachs W. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci U S A. 2004; 101: 14812-14817. PMID: 15465915
19. Mound L, Wheeler G, Williams D. Resolving cryptic species with morphology and DNA; thrips as a potential biocontrol agent of Brazilian peppertree, with a new species and overview of Pseudophilothrips (Thysanoptera). Zootaxa. 2010; 2432: 59-68.
20. Rugman-Jones PF, Hoddle MS, Stouthamer R. Nuclear-mitochondrial barcoding exposes the global pest western flower thrips (Thysanoptera: Thripidae) as two sympatric cryptic species in its native California. J Econ Entomol. 201; 103: 877-886. PMID: 20568635
21. Boykin LM, Armstrong KF, Kubatko L, De Barro P. Species delimitation and global biosecurity. Evol Bioinform Online. 2012; 8: 1-37. doi: 10.4137/EBO.S8532 PMID: 22267902
22. Dowton M, Meiklejohn K, Cameron SL, Wallman J. A preliminary framework for DNA barcoding, incorporating the multispecies coalescent. Syst Biol. 2014; 63: 639-644. doi: 10.1093/sysbio/syu028 PMID: 24682413
23. Worner SP, Gervey M. Modeling global insect pest species assemblages to determine risk of invasion. J Appl Ecol. 2006; 43: 858-867.
24. Dickey A, Shatters R, McKenzie C. A comparison of two methods of eluting insect DNA from flinders technology associates cards. Fla Entomol. 2012; 95: 790-793.
25. Hoddle MS, Mound LA. The genus Scirtothrips in Australia. Zootaxa. 2003; 268: 1-40.
26. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol. 1994; 3: 294-299. PMID: 7881515
27. Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annu Rev Ecol Evol Syst. 2006; 37: 545-579.
28. Ivanova NV, Zemlak TS, Hanner RH, Hebert PD. Universal primer cocktails for fish DNA barcoding. Mol Ecol Notes. 2007; 7: 544-548.
29. Shao R, Barker SC. The highly rearranged mitochondrial genome of the plague thrips Thrips imaginis (Insecta: Thysanoptera): convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes. Mol Biol Evol. 2003; 20: 362-370. PMID: 12644556
30. Hajibabaei M, Smith MA, Janzen DH, Rodriguez JJ, Whitfield JB, Hebert PDN. A minimalist barcode can identify a specimen whose DNA is degraded. Mol Ecol Notes. 2006; 6: 959-964.
31. Camacho C, Colulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinforma. 2009; 10: 421.
32. Dickey AM, Trease AJ, Jara-Cavieres A, Kumar V, Christenson MK, Potluri L-P, et al. Estimating bacterial diversity in Scirtothrips dorsalis Hood (Thysanoptera: Thripidae) via next generation sequencing. Fla Entomol. 2014; 92: 362-366.
33. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 2000; 132: 365-386. PMID: 10547847
34. Campbell B, Heraty J, Rasplus J, Chan K, Steffen-Campbell J, et al. Molecular systematics of the Chalcidoidea using 28S-D2 rDNA. In: Austin A, Dowton M, editors. The Hymenoptera: Evolution, Biodiversity and Biological Control. Melbourne: CSIRO publishing; 2000. pp. 57-71.
35. Stanke M, Morgenstern B. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 2005; 33: W465-W467. PMID: 15980513
36. Swofford DL. PAUP∗, Phylogenetic Analysis Using Parsimony (∗and other Methods). Sunderland, MA: Sinauer; 2003.
37. Dinsdale A, Cook L, Riginos C, Buckley YM, De Barro P. Refined global analysis of Bemisia tabaci (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidae) mitochondrial cytochrome oxidase 1 to identify species level genetic boundaries. Ann Entomol Soc Am. 2010; 103: 196-208.
38. Magnacca KN, Brown MJ. Mitochondrial heteroplasmy and DNA barcoding in Hawaiian Hylaeus (Nesoprosopis) bees (Hymenoptera: Colletidae). BMC Evol Biol. 2010; 10: 174. doi: 10.1186/1471-2148-10-174 PMID: 20540728
39. Rannala B, Yang Z. Improved reversible jump algorithms for Bayesian species delimitation. Genetics. 2013; 194: 245-253. doi: 10.1534/genetics.112.149039 PMID: 23502678
40. Yang Z, Rannala B. Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci USA. 2010; 107: 9264-9269. doi: 10.1073/pnas.0913022107 PMID: 20439743
41. Leaché AD, Fujita MK. Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proc R Soc Biol Sci Ser B. 2010; 277: 3071-3077. doi: 10.1098/rspb.2010.0662 PMID: 20519219
42. Xia X, Lemey P. Assessing substitution saturation with DAMBE. In: Lemey P, Salemi M, Vandamme A, editors. The Phylogenetic Handbook: a Practical Approach to DNA and Protein Phylogeny. 2nd ed: Cambridge University Press; 2009. pp. 615-630.
43. Xia X, Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J Hered. 2001; 92: 371-373. PMID: 11535656
44. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997; 24: 4876-4882. PMID: 9396791
45. Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. Version 2.74 [computer program]; 2001. Available: http://mesquite project.org. Accessed 2014 Aug 21.
46. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012; 61: 539-542. doi: 10.1093/sysbio/sys029 PMID: 22357727
47. Rambaut A, Drummond A. Tracer version 1.6 [computer program]; 2007. Available: http://tree.bio.ed.ac.uk/software/. Accessed 2014 Aug 21.
48. Lanfear R, Calcott B, Ho SY, Guindon S. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol. 2012; 29: 1695-1701. doi: 10.1093/ molbev/mss020 PMID: 22319168
49. Xie W, Lewis PO, Fan Y, Kuo L, Chen M-H. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst Biol. 2011; 60: 150-160. doi: 10.1093/sysbio/syq085 PMID: 21187451
50. Condamine FL, Toussaint EF, Cotton AM, Genson GS, Sperling FA, Kergoat GJ. Fine-scale biogeographical and temporal diversification processes of peacock swallowtails (Papilio subgenus Achillides) in the Indo-Australian Archipelago. Cladistics. 2013; 29: 88-111.
51. Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol. 2008; 25: 1253-1256. doi: 10.1093/molbev/msn083 PMID: 18397919
52. Sukumaran J, Holder MT. DendroPy: a Python library for phylogenetic computing. Bioinformatics. 2010; 26: 1569-1571. doi: 10.1093/bioinformatics/btq228 PMID: 20421198
53. Rambaut A. FigTree, a graphical viewer of phylogenetic trees. Version 1.4 [computer program]; 2007. Available: http://tree.bio.ed.ac.uk/software/. Accessed 2014 Aug 21.
54. Mound LA, Stiller M. Species of the genus Scirtothrips from Africa (Thysanoptera, Thripidae). Zootaxa. 2011; 2786: 51-61.
55. Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009; 25: 1451-1452. doi: 10.1093/bioinformatics/btp187 PMID: 19346325
56. Excoffier L, Lischer HE. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res. 2010; 10: 564-567. doi: 10.1111/j.1755-0998.2010.02847.x PMID: 21565059
57. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993; 10: 512-526. PMID: 8336541
58. Rogers AR, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol. 1992; 9: 552-569. PMID: 1316531
59. Harpending H. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol. 1994; 66: 591-600. PMID: 8088750
60. Ramos-Onsins SE, Rozas J. Statistical properties of new neutrality tests against population growth. Mol Biol Evol. 2002; 19: 2092-2100. PMID: 12446801
61. Fu Y-X, Li W-H. Statistical tests of neutrality of mutations. Genetics. 1993; 133: 693-709. PMID: 8454210
62. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989; 123: 585-595. PMID: 2513255
63. Fu Y-X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 1997; 147: 915-925. PMID: 9335623
64. Seal D, Klassen W, Kumar V. Biological parameters of Scirtothrips dorsalis (Thysanoptera: Thripidae) on selected hosts. Environ Entomol. 2010; 39: 1389-1398. doi: 10.1603/EN09236 PMID: 22546433
65. Kittler R, Kayser M, Stoneking M. Molecular evolution of Pediculus humanus and the origin of clothing. Curr Biol. 2003; 13: 1414-1417. PMID: 12932325
66. Schenekar T, Weiss S. High rate of calculation errors in mismatch distribution analysis results in numerous false inferences of biological importance. Heredity. 2011; 107: 511. doi: 10.1038/hdy.2011.48 PMID: 21731052
67. Shao R, Dowton M, Murrell A, Barker SC. Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects. Mol Biol Evol. 2003; 20: 1612-1619. PMID: 12832626
68. Brower A. Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution. Proc Natl Acad Sci USA. 1994; 91: 6491-6495. PMID: 8022810
69. Papadopoulou A, Anastasiou I, Vogler AP. Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration. Mol Biol Evol. 2010; 27: 1659-1672. doi: 10.1093/molbev/msq051 PMID: 20167609
70. Kass RE, Raftery AE. Bayes factors. J Am Statist Assoc 1995; 90: 773-795.
71. Hebert PD, Cywinska A, Ball SL. Biological identifications through DNA barcodes. Proc R Soc Biol Sci Ser B. 2003; 270: 313-321.
72. Rubinoff D. Utility of mitochondrial DNA barcodes in species conservation. Conserv Biol 2006; 20: 1026-1033. PMID: 16922219
73. Jinbo U, Kato T, Ito M. Current progress in DNA barcoding and future implications for entomology. Entomol Sci. 2011; 14: 107-124.
74. Carolan JC, Murray TE, Fitzpatrick Ú, Crossley J, Schmidt H, Cederberg B, et al. Colour patterns do not diagnose species: quantitative evaluation of a DNA barcoded cryptic bumblebee complex. PLoS ONE. 2012; 7: e29251. doi: 10.1371/journal.pone.0029251 PMID: 22238595
75. Song H, Buhay JE, Whitting MF, Crandall KA. Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Nat Acad Sci USA. 2008; 105: 13486-13491. doi: 10.1073/pnas.0803076105 PMID: 18757756
76. Peccoud J, Ollivier A, Plantegenest M, Simon JC. A continuum of genetic divergence from sympatric host races to species in the pea aphid complex. Proc Natl Acad Sci USA. 2009; 106: 7495-7500. doi: 10.1073/pnas.0811117106 PMID: 19380742
77. Hoddle MS, Mound LA, Rugman-Jones PF, Stouthamer R. Synonomy of five Scirtothrips species (Thysanoptera: Thripidae) described from Avocados (Persea americana) in Mexico. Fla Entomol. 2008; 91: 16-21.
78. Meissner H, Lemay A, Borchert D, Nietschke B, Neeley A, Magarey R, et al. Evaluation of possible pathways of introduction for Scirtothrips dorsalis Hood (Thysanoptera: Thripidae) from the Caribbean into the continental United States. Raleigh: Center for Plant Health Science and Technology, Plant Epidemiology and Risk Assessment Laboratory; 2005.
79. Riley DG, Joseph SV, Srinivasan R, Diffle S. Thrips vectors of tospoviruses. J Integ Pest Mngmt. 2011; 1: 2011; doi: 2010.1603/IPM10020
80. Gopal K, Reddy MK, Reddy DVR, Muniyappa V. Transmission of peanut yellow spot virus (PYSV) by thrips, Scirtothrips dorsalis Hood in groundnut. Arch Phytopathol Plant Protect. 2010; 43: 421-429.
81. Amin PW, Reddy DVR, Ghanekar AM. Transmission of tomato spotted wilt virus, the causal agent of bud necrosis of peanut, by Scirtothrips dorsalis and Frankliniella schultzei. Plant Diseases. 1981; 65: 663-665.
82. Chiemsombat P, Gajanandana O, Warin N, Hongprayoon R, Bhunchoth A, Pongsapich P. Biological and molecular characterization of tospoviruses in Thailand. Arch Virol. 2008; 153: 571-577. doi: 10.1007/s00705-007-0024-3 PMID: 18188501
83. Chu F-H, Chao C-H, Peng Y-C, Lin S-S, Chen C-C, Yeh S-D. Serological and Molecular Characterization of Peanut chlorotic fan-spot virus, a new species of the genus Tospovirus. Phytopathology. 2001; 91: 856-863. doi: 10.1094/PHYTO.2001.91.9.856 PMID: 18944231
84. Nietschke BS, Borchert DM, Magarey RD, Ciomperlik MA. Climatological potential for Scirtothrips dorsalis (Thysanoptera: Thripidae) establishment in the United States. Fla Entomol. 2008; 91: 79-86.
85. Venette RC, Davis EE. Mini risk assessment: Chili thrips/yellow tea thrips, Scirtothrips dorsalis Hood (Thysanoptera: Thripidae). St. Paul: Department of Entomology, University of Minnesota; 2004.
86. Minamikawa J. The thrips of the tea plant. Tea Res J. 1960; 16: 23-26.