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Population differentiation between Australian and Chinese Helicoverpa armigera occurs in distinct blocks on the Z-chromosome

  • S.V. Song (a1) (a2), C. Anderson (a3) (a4), R.T. Good (a1) (a2), S. Leslie (a1) (a5) (a6), Y. Wu (a7), J.G. Oakeshott (a4) and C. Robin (a1) (a2)...

Over the last 40 years, many types of population genetic markers have been used to assess the population structure of the pest moth species Helicoverpa armigera. While this species is highly vagile, there is evidence of inter-continental population structure. Here, we examine Z-chromosome molecular markers within and between Chinese and Australian populations. Using 1352 polymorphic sites from 40 Z-linked loci, we compared two Chinese populations of moths separated by 700 km and found virtually no population structure (n = 41 and n = 54, with <1% of variation discriminating between populations). The levels of nucleotide diversity within these populations were consistent with previous estimates from introns in Z-linked genes of Australian samples (π = 0.028 vs. 0.03). Furthermore, all loci surveyed in these Chinese populations showed a skew toward rare variants, with ten loci having a significant Tajima's D statistic, suggesting that this species could have undergone a population expansion. Eight of the 40 loci had been examined in a previous study of Australian moths, of which six revealed very little inter-continental population structure. However, the two markers associated with the Cyp303a1 locus that has previously been proposed to be a target of a selective sweep, exhibited allele structuring between countries. Using a separate dataset of 19 Australian and four Chinese moths, we scanned the molecular variation distributed across the entire Z-chromosome and found distinct blocks of differentiation that include the region containing Cyp303a1. We recommend some of these loci join those associated with insecticide resistance to form a set of genes best suited to analyzing population structure in this global pest.

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Anderson C.J., Tay W.T., McGaughran A., Gordon K. & Walsh T.K. (2016) Population structure and gene flow in the global pest, Helicoverpa armigera . Molecular Ecology 25(21), 52965311.
Arnemann J.A., James W.J., Walsh T.K., Guedes J.V.C., Smagghe G., Castiglioni E. & Tay W.T. (2016) Mitochondrial DNA COI characterization of Helicoverpa armigera (Lepidoptera: Noctuidae) from Paraguay and Uruguay. Genetics and Molecular Research 15, 15028292.
Baird N.A., Etter P.D., Atwood T.S., Currey M.C., Shiver A.L., Lewis Z.A., Selker E.U., Cresko W.A. & Johnson E.A. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3, e3376, doi: 10.1371/journal.pone.0003376.
Battlay P., Schmidt J.M., Fournier-Level A. & Robin C. (2016) Genomic and transcriptomic associations identify a new insecticide resistance phenotype for the selective sweep at the Cyp6g1 locus of Drosophila melanogaster . G3 (Bethesda) 6, 25732581.
Behere G., Tay W., Russell D., Heckel D., Appleton B., Kranthi K. & Batterham P. (2007) Mitochondrial DNA analysis of field populations of Helicoverpa armigera (Lepidoptera: Noctuidae) and of its relationship to H. zea. BMC Evolutionary Biology 7, 117.
Behere G.T., Tay W.T., Russell D.A., Kranthi K.R. & Batterham P. (2013) Population genetic structure of the cotton bollworm Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in India as inferred from EPIC-PCR DNA markers. PLoS ONE 8, e53448. ISSN . doi: 10.1371/journal.pone.0053448.
Browning S. R. & Browning B. L. (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. The American Journal of Human Genetics 81, 10841097.
Buss D. S. & Callaghan A. (2008) Interaction of pesticides with p-glycoprotein and other ABC proteins: a survey of the possible importance to insecticide, herbicide and fungicide resistance. Pesticide Biochemistry and Physiology 90, 141153.
Charlesworth B., Coyne J.A. & Barton N.H. (1987) The relative rates of evolution of sex chromosomes and autosomes. American Naturalist 130, 113146.
Cho S., Mitchell A., Mitter C., Regier J., Matthews M. & Robertson R. (2008) Molecular phylogenetics of heliothine moths (Lepidoptera: Noctuidae: Heliothinae), with comments on the evolution of host range and pest status. Systematic Entomology 33, 581594.
Collart M.A. & Panasenko O.O. (2012) The CCR4-Not complex. Gene 492, 4253.
Common I. (1953) The Australian species of Heliothis (Lepidoptera: Noctuidae) and their pest status. Australian Journal of Zoology 1, 319344.
Czepak C., Albernaz K.C., Vivan L.M., Guimarães H.O. & Carvalhais T. (2013) First reported occurrence of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in Brazil. Pesquisa Agropecuária Tropical 43, 110113.
Daly J.C. (1993) Ecology and genetics of insecticide resistance in Helicoverpa armigera: interactions between selection and gene flow. Genetica 90, 217226.
Daly J.C. & Fisk J.H. (1998) Sex-linked inheritance of endosulphan resistance in Helicoverpa armigera . Heredity 81, 5562.
Danecek P., Auton A., Abecasis G., Albers C.A., Banks E., DePristo M.A., Handsaker R.E., Lunter G., Marth G.T., Sherry S.T. & McVean G. (2011) The variant call format and VCFtools. Bioinformatics 27, 21562158.
Earl D.A. & vonHoldt B.M. (2011) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4, 359361.
Elshire R.J., Glaubitz J.C., Sun Q., Poland J.A., Kawamoto K., Buckler E.S. & Mitchell S.E. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6, e19379. doi: 10.1371/journal.pone.0019379.
Evanno G., Regnaut S. & Goudet J. (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 26112620.
Falush D., Wirth T., Linz B., Pritchard J.K., Stephens M., Kidd M., Blaser M.J., Graham D.Y., Vacher S., Perez-Perez G.I., Yamaoka Y., Mégraud F., Otto K., Reichard U., Katzowitsch E., Wang X., Achtman M. & Suerbaum S. (2003) Traces of human migrations in Helicobacter pylori populations. Science 299, 15821585.
Fitt G.P. (1994) Cotton pest management: Part 3. An Australian perspective. Annual Review of Entomology 39, 543562.
Gahan L.J., Gould F. & Heckel D.G. (2001) Identification of a gene associated with Bt resistance in Heliothis virescens . Science 293, 857860.
Gahan L.J., Pauchet Y., Vogel H. & Heckel D.G. (2010) An ABC transporter mutation is correlated with insect resistance to Bacillus thuringiensis Cry1ac toxin. PLoS Genetics 6, e1001248. doi: 10.1371/ journal.pgen.1001248.
Garud N.R., Messer P.W., Buzbas E.O. & Petrov D.A. (2015) Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps. PLoS Genetics 11, e1005004. doi: 10.1371/journal.pgen. 1005004.
Gilles A., Meglécz E., Pech N., Ferreira S., Malausa T. & Martin J.F. (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12, 245.
Gordon K.H.J., Tay W.T., Collinge D., Williams A. & Batterham P. (2010) Genetics and molecular biology of the major crop pest genus Helicoverpa . pp. 219238 in Goldsmith M.R. & Marec F. (Eds) Molecular Biology and Genetics of the Lepidoptera. CRC Press, Boca Raton, FL, USA ISBN 978-1-4200-6020-1.
Goudet J. (2005). HIERFSTAT, a package for R to compute and test hierarchical F-statistics. Molecular Ecology Resources 5, 184186.
Gouy M., Guindon S. & Gascuel O. (2010) Seaview version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27, 221224.
Green R.E., Krause J., Briggs A.W., Maricic T., Stenzel U., Kircher M., Patterson N., Li H., Zhai W., Fritz M.H.Y., Hansen N.F., Durand E.Y., Malaspinas A.S., Jensen J.D., Marques-Bonet T., Alkan C., Prüfer K., Meyer M., Burbano H.A., Good J.M., Schultz R., Aximu-Petri A., Butthof A., Höber B., Höffner B., Siegemund M., Weihmann A., Nusbaum C., Lander E.S., Russ C., Novod N., Affourtit J., Egholm M., Verna C., Rudan P., Brajkovic D., Kucan , Gušic I., Doronichev V.B., Golovanova L.V., Lalueza-Fox C., de la Rasilla M., Fortea J., Rosas A., Schmitz R.W., Johnson P.L.F., Eichler E.E., Falush D., Birney E., Mullikin J.C., Slatkin M., Nielsen R., Kelso J., Lachmann M., Reich D. & Pääbo S. (2010) A draft sequence of the Neandertal genome. Science 328, 710722.
Head D.J., McCaffery A.R. & Callaghan A. (1998) Novel mutations in the para-homologous sodium channel gene associated with phenotypic expression of nerve insensitivity resistance to pyrethroids in Heliothine lepidoptera. Insect Molecular Biology 7, 191196.
Hill W.G. & Weir B.S. (1988) Variances and covariances of squared linkage disequilibria in finite populations. Theoretical Population Biology 33, 5478.
Jombart T. & Ahmed I. (2011) Adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27, 30703071.
Joußen N., Agnolet S., Lorenz S., Schöne S.E., Ellinger R., Schneider B. & Heckel D.G. (2012) Resistance of Australian Helicoverpa armigera to fenvalerate is due to the chimeric P450 enzyme CYP337B3. Proceedings of the National Academy of Sciences 109, 1520615211.
Kamvar Z.N., Tabima J.F. & Grünwald N.J. (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2, e281. ISSN . doi: 10.7717/peerj.281.
Lakey A., Labeit S., Gautel M., Ferguson C., Barlow D.P., Leonard K. & Bullard B. (1993) Kettin, a large modular protein in the Z-disc of insect muscles. The EMBO Journal 12, 28632871.
Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J. & Higgins D.G. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23, 29472948.
Leite N.A., Alves-Pereira A., Corrêa A.S., Zucchi M.I. & Omoto C. (2014) Demographics and genetic variability of the New World bollworm (Helicoverpa zea) and the Old World bollworm (Helicoverpa armigera) in Brazil. PLoS ONE 9, e113286. ISSN . doi: 10.1371/journal.pone. 0113286.
Mallet J., Korman A., Heckel D.G. & King P. (1993) Biochemical genetics of Heliothis and Helicoverpa (Lepidoptera: Noctuidae) and evidence for a founder event in Helicoverpa zea . Annals of the Entomological Society of America 86, 189197.
Martinez-Torres D., Devonshire A.L. & Williamson M.S. (1997) Molecular studies of knockdown resistance to pyrethroids: cloning of domain II sodium channel gene sequences from insects. Pesticide Science 51, 265270.
Mastrangelo T., Paulo D.F., Bergamo L.W., Morais E.G.F., Silva M., Bezerra-Silva G. & Azeredo-Espin A.M.L. (2014) Detection and genetic diversity of a heliothine invader (Lepidoptera: Noctuidae) from north and northeast of Brazil. Journal of Economic Entomology 107, 970980.
Matthews M. (1999) Heliothine moths of Australia: a guide to pest bollworms and related noctuid groups. Monographs on Australian Lepidoptera, Vol. 7. Melbourne, CSIRO Publishing. ISBN 0-643-06305-6.
McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M. & DePristo M.A. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20, 12971303.
Mitchell A. & Gopurenko D. (2016) DNA barcoding the Heliothinae (Lepidoptera: Noctuidae) of Australia and utility of DNA barcodes for pest identification in Helicoverpa and relatives. PLoS ONE 11, e0160895. ISSN . doi: 10.1371/journal.pone.0160895.
Murúa M.G., Scalora F.S., Navarro F.R., Cazado L.E., Casmuz A., Villagrán M.E., Lobos E. & Gastaminza G. (2014) First record of Helicoverpa armigera (Lepidoptera: Noctuidae) in Argentina. Florida Entomologist 97, 854856.
Nibouche S., Bues R., Toubon J.F. & Poitout S. (1998) Allozyme polymorphism in the cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae): comparison of African and European populations. Heredity 80, 438445.
Nielsen R. (2005) Molecular signatures of natural selection. Annual Review Of Genetics 39, 197218.
Pearce S.L., Clarke D.F., East P.D., Elfekih S., Gordon K.H.J., Jermiin L.S., McGaughran A., Oakeshott J.G., Papanikolaou A., Perera O.P., Rane R.V., Richards S., Tay W.T., Walsh T.K., Anderson A., Anderson C.J., Asgari S., Board P.G., Bretschneider A., Campbell P.M., Chertemps T., Christeller J.T., Coppin C.W., Downes S.J., Duan G., Farnsworth C.A., Good R.T., Han L.B., Han Y.C., Hatje K., Horne I., Huang Y.P., Hughes D.S.T., Jacquin-Joly E., James W., Jhangiani S., Kollmar M., Kuwar S.S., Li S., Liu N.Y., Maibeche M.T., Miller J.R., Montagne N., Perry T., Qu J., Song S.V., Sutton G.G., Vogel H., Walenz B.P., Xu W., Zhang H.J., Zou Z., Batterham P., Edwards O.R., Feyereisen R., Gibbs R.A., Heckel D.G., McGrath A., Robin C., Scherer S.E., Worley K.C. and Wu Y.D. (2017) Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. BMC Biology 15, 63.
Pritchard J.K., Stephens M. & Donnelly P. (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945959.
Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M. A., Bender D., Maller J., Sklar P., De Bakker P.I., Daly M.J. & Sham P. C. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics 81, 559575.
Rašić G., Filipović I., Weeks A. R. & Hoffmann A. A. (2014) Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti . BMC Genomics 15, 275.
R Core Team (2014) R: A Language and Environment for Statistical Computing. Vienna, Austria, R Foundation for Statistical Computing.
Reinhardt J.A., Kolaczkowski B., Jones C.D., Begun D.J. & Kern A.D. (2014) Parallel geographic variation in Drosophila melanogaster . Genetics 197, 361373.
Rohland N. & Reich D. (2012) Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Research 22, 939946.
Rozas J., Sanchez-DelBarrio J.C., Messeguer X. & Rozas R. (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 24962497.
Sackton T.B., Corbett-Detig R.B., Nagaraju J., Vaishna L., Arunkumar K.P. & Hartl D.L. (2014) Positive selection drives faster-Z evolution in silkmoths. Evolution 68, 23312342.
Slatkin M. (2008) Linkage disequilibrium – understanding the evolutionary past and mapping the medical future. Nature Reviews Genetics 9, 477485.
Song S.V., Downes S., Parker T., Oakeshott J.G. & Robin C. (2015) High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep. Heredity (Edinb) 115, 460470.
Sosa-Gómez D.R., Specht A., Paula-Moraes S.V., Lopes-Lima A., Yano S.A.C., Micheli A., Morais E.G.F., Gallo P., Pereira P.R.V.S., Sal-vadori J.R., Botton M., Zenker M.M. & Azevedo-Filho W.S. (2016) Timeline and geographical distribution of Helicoverpa armigera (Hübner) (Lepidoptera, Noctuidae: Heliothinae) in Brazil. Revista Brasileira de Entomologia 60, 101104.
Srinivas R., Udikeri S. S., Jayalakshmi S. K. & Sreeramulu K. (2004) Identification of factors responsible for insecticide resistance in Helicoverpa armigera . Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 137, 261269.
Staubach F., Lorenc A., Messer P.W., Tang K., Petrov D.A. & Tautz D. (2012) Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS Genetics 8, e1002891.
Tabashnik B.E., Gould F. & Carrière Y. (2004) Delaying evolution of insect resistance to transgenic crops by decreasing dominance and heritability. Journal of Evolutionary Biology 17, 904912.
Tay W., Behere G., Batterham P. & Heckel D. (2010) Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes. BMC Evolutionary Biology 10, 144.
Tay W.T., Soria M.F., Walsh T., Thomazoni D., Silvie P., Behere G.T., Anderson C. & Downes S. (2013) A brave new world for an Old World pest: Helicoverpa armigera (Lepidoptera: Noctuidae) in Brazil. PLoS ONE 8, e80134. doi: 10.1371/journal.pone.0080134.
Vicoso B. & Charlesworth B. (2006) Evolution on the X chromosome: unusual patterns and processes. Nature Reviews Genetics 7, 645653.
Wallar B.J. & Alberts A.S. (2003) The formins: active scaffolds that remodel the cytoskeleton. Trends in Cell Biology 13, 435446.
Wickham H. (2009) ggplot2: Elegant Graphics for Data Analysis, vol. 1. New York, Springer, p. 3.
Zhang D.X. (2004) Lepidopteran microsatellite DNA: redundant but promising. Trends in Ecology & Evolution 19, 507509.
Zhou X., Faktor O., Applebaum S.W. & Coll M. (2000) Population structure of the pestiferous moth Helicoverpa armigera in the Eastern Mediterranean using RAPD analysis. Heredity 85, 251256.
Zhu L., Tatsuke T., Li Z., Mon H., Xu J., Lee J.M. & Kusakabe T. (2012) Molecular cloning of BmTUDOR-SN and analysis of its role in the RNAi pathway in the silkworm, Bombyx mori (Lepidoptera: Bombycidae). Applied Entomology and Zoology 47, 207215.
Zhu L., Tatsuke T., Mon H., Li Z., Xu J., Lee J.M. & Kusakabe T. (2013) Characterization of Tudor-SN-containing granules in the silkworm, Bombyx mori . Insect Biochemistry and Molecular Biology 43, 664674.
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