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Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control

  • 1.

    Traugott, M., Benefer, C. M., Blackshaw, R. P., van Herk, W. G. & Vernon, R. S. Biology, ecology, and control of elaterid beetles in agricultural land. Annu. Rev. Entomol. 60, 313–334 (2015).

    CAS  PubMed  Google Scholar 

  • 2.

    Knodel, J. J. & Shrestha, G. Pulse crops: pest management of wireworms and cutworms in the Northern Great Plains of United States and Canada. Ann. Entomological Soc. Am. 111, 195–204 (2018).

    Google Scholar 

  • 3.

    Vernon, R. S. et al. Transitional sublethal and lethal effects of insecticides after dermal exposures to five economic species of wireworms (Coleoptera: Elateridae). J. Economic Entomol. 101, 365–374 (2008).

    CAS  Google Scholar 

  • 4.

    Reddy, G. V. P. & Tangtrakulwanich, K. Potential application of pheromones in monitoring, mating disruption, and control of click beetles (Coleoptera: Elateridae). ISRN Entomol. 2014, 1–8 (2014).

    Google Scholar 

  • 5.

    Morales-Rodriguez, A. & Wanner, K. W. Efficacy of thiamethoxam and fipronil, applied alone and in combination, to control Limonius californicus and Hypnoidus bicolor (Coleoptera: Elateridae). Pest Manag. Sci. 71, 584–591 (2015).

    CAS  PubMed  Google Scholar 

  • 6.

    van Herk, W. G., Vernon, R. S., Tolman, J. H. & Saavedra, H. O. Mortality of a wireworm, Agriotes obscurus (Coleoptera: Elateridae), after topical application of various insecticides. J. Economic Entomol. 101, 375–383 (2008).

    Google Scholar 

  • 7.

    Vernon, R. S., Van Herk, W. G., Clodius, M. & Harding, C. Wireworm management I: stand protection versus wireworm mortality with wheat seed treatments. J. Economic Entomol. 102, 2126–2136 (2009).

    CAS  Google Scholar 

  • 8.

    Vernon, R. S., Van Herk, W. G., Clodius, M. & Harding, C. Further studies on wireworm management in Canada: damage protection versus wireworm mortality in potatoes. J. Economic Entomol. 106, 786–799 (2013).

    CAS  Google Scholar 

  • 9.

    van Herk, W. G. et al. Contact behaviour and mortality of wireworms exposed to six classes of insecticide applied to wheat seed. J. Pest Sci. 88, 717–739 (2015).

    Google Scholar 

  • 10.

    van Herk, W. G., Labun, T. J. & Vernon, R. S. Efficacy of diamide, neonicotinoid, pyrethroid, and phenyl pyrazole insecticide seed treatments for controlling the sugar beet wireworm, Limonius californicus (Coleoptera: Elateridae), in spring wheat. J. Entomological Soc. Br. Columbia 115, 86–100 (2019).

    Google Scholar 

  • 11.

    Ensafi, P. et al. Soil type mediates the effectiveness of biological control against Limonius californicus (Coleoptera: Elateridae). J. Economic Entomol. 111, 2053–2058 (2018).

    CAS  Google Scholar 

  • 12.

    Stern, V. M. S. R., van den Bosch, R. & Hagen, K. S. The integrated control concept. Hilgardia 29, 81–101 (1959).

    CAS  Google Scholar 

  • 13.

    Barzman, M. et al. Eight principles of integrated pest management. Agron. Sustain. Dev. 35, 1199–1215 (2015).

    Google Scholar 

  • 14.

    Hebert, P. D. N., Cywinska, A., Ball, S. L. & DeWaard, J. R. Biological identifications through DNA barcodes. Proc. R. Soc. B-Biol. Sci. 270, 313–321 (2003).

    CAS  Google Scholar 

  • 15.

    Zhang, S. K. et al. DNA barcoding identification and genetic diversity of bamboo shoot wireworms (Coleoptera: Elateridae) in South China. J. Asia-Pac. Entomol. 22, 140–150 (2019).

    Google Scholar 

  • 16.

    Ellis, J. S., Blackshaw, R., Parker, W., Hicks, H. & Knight, M. E. Genetic identification of morphologically cryptic agricultural pests. Agric. For. Entomol. 11, 115–121 (2009).

    Google Scholar 

  • 17.

    Benefer, C. M. et al. The molecular identification and genetic diversity of economically important wireworm species (Coleoptera: Elateridae) in Canada. J. Pest Sci. 86, 19–27 (2013).

    Google Scholar 

  • 18.

    Etzler, F. E., Wanner, K. W., Morales-Rodriguez, A. & Ivie, M. A. DNA barcoding to improve the species-level management of wireworms (Coleoptera: Elateridae). J. Economic Entomol. 107, 1476–1485 (2014).

    Google Scholar 

  • 19.

    Lindroth, E. & Clark, T. L. Phylogenetic analysis of an economically important species complex of wireworms (Coleoptera: Elateridae) in the midwest. J. Economic Entomol. 102, 743–749 (2009).

    CAS  Google Scholar 

  • 20.

    Allendorf, F. W. Genetics and the conservation of natural populations: allozymes to genomes. Mol. Ecol. 26, 420–430 (2017).

    CAS  PubMed  Google Scholar 

  • 21.

    Savolainen, O., Lascoux, M. & Merila, J. Ecological genomics of local adaptation. Nat. Rev. Genet. 14, 807–820 (2013).

    CAS  PubMed  Google Scholar 

  • 22.

    Rashed, A., Etzler, F., Rogers, C. W. & Marshall, J. M. Wireworms in Idaho Cereals: Monitoring and Identification 898 (University of Idaho Extension Bulletin, 2015).

  • 23.

    Milosavljevic I., Esser A. D. & Crowder D. W. Identifying Wireworms in Cereal Crops FS175E (Washington State University Extension, 2015).

  • 24.

    Stone, M. W. Life History of the Sugar-beet Wireworm in Southern California. Tech. Bull. No. 744 (1941).

  • 25.

    Andrews, K., Good, J., Miller, M., Luikart, G. & Hohenlohe, P. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat. Rev. Genet. 17, 81–92 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 26.

    Coissac, E., Hollingsworth, P. M., Lavergne, S. & Taberlet, P. From barcodes to genomes: extending the concept of DNA barcoding. Mol. Ecol. 25, 1423–1428 (2016).

    CAS  PubMed  Google Scholar 

  • 27.

    Miller, J. M., Malenfant, R. M., Moore, S. S. & Coltman, D. W. Short reads, circular genome: Skimming SOLiD sequence to construct the bighorn sheep mitochondrial genome. J. Heredity 103, 140–146 (2012).

    CAS  Google Scholar 

  • 28.

    McVean, G. A genealogical interpretation of principal components analysis. PLoS Genet. 5, e1000686 (2009).

  • 29.

    Wang, J. Triadic IBD coefficients and applications to estimating pairwise relatedness. Genet. Res. 89, 135–153 (2007).

    CAS  PubMed  Google Scholar 

  • 30.

    Papadopoulou, A., Anastasiou, I. & Vogler, A. P. Revisiting the insect mitochondrial molecular clock: The mid-Aegean trench calibration. Mol. Biol. Evolution 27, 1659–1672 (2010).

    CAS  Google Scholar 

  • 31.

    Hebert, P. D. N., Ratnasingham, S. & deWaard, J. R. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. B-Biol. Sci. 270, S96–S99, (2003).

    CAS  Google Scholar 

  • 32.

    Huemer, P. et al. Large geographic distance versus small DNA barcode divergence: insights from a comparison of European to South Siberian Lepidoptera. PLoS One 13, e0206668 (2018).

  • 33.

    Sun, S. E. et al. DNA barcoding reveal patterns of species diversity among northwestern Pacific molluscs. Sci. Rep. 6, 33367 (2016).

  • 34.

    Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R. & Hebert, P. D. N. DNA barcoding Australia’s fish species. Philos. Trans. R. Soc. B-Biol. Sci. 360, 1847–1857 (2005).

    CAS  Google Scholar 

  • 35.

    Brunsfeld, S. J., Sullivan, J., Soltis, D. E. & Soltis, P. S. in Integrating Ecological and Evolutionary Processes in A Spatial Context Vol. 14 (eds Silvertown, J. & Antonovics, J.) 319–339 (Blackwell Science, Oxford, 2001).

  • 36.

    Rankin, A. M. et al. Complex interplay of ancient vicariance and recent patterns of geographical speciation in north-western North American temperate rainforests explains the phylogeny of jumping slugs (Hemphillia spp.). Biol. J. Linn. Soc. 127, 876–889 (2019).

    Google Scholar 

  • 37.

    Maroja, L. S., Bogdanowicz, S. M., Wallin, K. F., Raffa, K. F. & Harrison, R. G. Phylogeography of spruce beetles (Dendroctonus rufipennis Kirby) (Curculionidae: Scolytinae) in north america. Mol. Ecol. 16, 2560–2573 (2007).

    CAS  PubMed  Google Scholar 

  • 38.

    Arakaki, N., Hokama, Y. & Yamamura, K. Estimation of the dispersal ability of Melanotus okinawensis (Coleoptera: Elateridae) larvae in soil. Appl. Entomol. Zool. 45, 297–302 (2010).

    Google Scholar 

  • 39.

    Schallhart, N., Tusch, M. J., Staudacher, K., Wallinger, C. & Traugott, M. Stable isotope analysis reveals whether soil-living elaterid larvae move between agricultural crops. Soil Biol. Biochem. 43, 1612–1614 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 40.

    Arakaki, N. et al. Estimation of abundance and dispersal distance of the sugarcane click beetle Melanotus sakishimensis Ohira (Coleoptera: Elateridae) on Kurima Island, Okinawa, by mark-recapture experiments. Appl. Entomol. Zool. 43, 409–419 (2008).

    Google Scholar 

  • 41.

    Schallhart, N., Wallinger, C., Juen, A. & Traugott, M. Dispersal abilities of adult click beetles in arable land revealed by analysis of carbon stable isotopes. Agric. For. Entomol. 11, 333–339 (2009).

    Google Scholar 

  • 42.

    Blackshaw, R. P., Vernon, R. S. & Thiebaud, F. Large scale Agriotes spp. click beetle (Coleoptera: Elateridae) invasion of crop land from field margin reservoirs. Agric. For. Entomol. 20, 51–61 (2018).

    Google Scholar 

  • 43.

    Hicks, H. & Blackshaw, R. P. Differential responses of three Agriotes click beetle species to pheromone traps. Agric. For. Entomol. 10, 443–448 (2008).

    Google Scholar 

  • 44.

    Rondon, S. I., Pantoja, A., Hagerty, A. & Horneck, D. A. Ground beelte (Coleoptera: Carabidae) populations in commercial organic and conventional potato production. Fla. Entomologist 96, 1492–1499 (2013).

    Google Scholar 

  • 45.

    Horton, D. R. & Landolt, P. J. Use of Japanese-beetle traps to monitor flight of the Pacific coast wireworm, Limonius canus (Coleoptera: Elateridae), and effects of trap height and color. J. Entomological Soc. Br. Columbia 98, 235–242 (2001).

    Google Scholar 

  • 46.

    Balkenhol, N., Cushman, S. A., Storfer, A. & Waits, L. P. Landscape Genetics—Concepts, Methods, Applications (John Wiley & Sons Ltd, West Sussex, 2016).

  • 47.

    Milosavljevic, I., Esser, A. D. & Crowder, D. W. Seasonal population dynamics of wireworms in wheat crops in the Pacific Northwestern United States. J. Pest Sci. 90, 77–86 (2017).

    Google Scholar 

  • 48.

    Gerritsen, A. T. et al. Full mitochondrial genome sequence of the sugar beet wireworm Limonius californicus (Coleoptera: Elateridae), a common agricultural pest. Microbiology Resource Announcements 4 (2016).

  • 49.

    Voskoboynik, A. et al. The genome sequence of the colonial chordate, Botryllus schlosseri. Elife 2, e00569 (2013).

  • 50.

    McCoy, R. C. et al. Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS ONE 9, e106689 (2014).

  • 51.

    Marzachi, C., Veratti, F. & Bosco, D. Direct PCR detection of phytoplasmas in experimentally infected insects. Ann. Appl. Biol. 133, 45–54 (1998).

    CAS  Google Scholar 

  • 52.

    Ali, O. A. et al. RAD Capture (Rapture): flexible and efficient sequence-based genotyping. Genetics 202, 389–400 (2016).

    CAS  PubMed  Google Scholar 

  • 53.

    Baym, M. et al. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS ONE 10, e0128036 (2015).

  • 54.

    Zimin, A. V. et al. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm. Genome Res. 27, 787–792 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 55.

    Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).

    PubMed  Google Scholar 

  • 56.

    Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A. & Cresko, W. A. Stacks: an analysis tool set for population genomics. Mol. Ecol. 22, 3124–3140 (2013).

    PubMed  PubMed Central  Google Scholar 

  • 57.

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 58.

    Poplin, R. et al. Scaling accurate genetic variant discovery to tens of thousands of samples. bioRxiv https://doi.org/10.1101/201178 (2017).

  • 59.

    Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

  • 60.

    Frichot, E. & Francois, O. LEA: an R package for landscape and ecological association studies. Methods Ecol. Evolution 6, 925–929 (2015).

    Google Scholar 

  • 61.

    R_Core_Team. R: A Language and Environment for Statistical Computing. http://www.R-project.org/ (R Foundation for Statistical Computing, Vienna, 2018).

  • 62.

    Excoffier, L., Laval, L. G. & Schneider, S. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolut. Bioinforma. Online 1, 47–50 (2005).

    CAS  Google Scholar 

  • 63.

    Jombart, T. & Ahmed, I. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27, 3070–3071 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 64.

    Wang, J. L. COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Mol. Ecol. Resour. 11, 141–145 (2011).

    PubMed  Google Scholar 

  • 65.

    Whitlock, M. C. & Lotterhos, K. E. Reliable detection of loci responsible for local adaptation: Inference of a null model through trimming the distribution of FST. Am. Naturalist 186, S24–S36 (2015).

    Google Scholar 

  • 66.

    Foll, M. & Gaggiotti, O. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180, 977–993 (2008).

    PubMed  PubMed Central  Google Scholar 

  • 67.

    Beaumont, M. A. & Nichols, R. A. Evaluating loci for use in the genetic analysis of population structure. Proc. R. Soc. Ser. B, Biol. Sci. 263, 1619–1626 (1996).

    Google Scholar 

  • 68.

    Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 69.

    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 70.

    Bouckaert, R. et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15, e1006650 (2019).

  • 71.

    Darriba, D., Taboada, G., Doallo, R. & Posada, D. jModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 9, 772 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 72.

    Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 


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