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Full List of Publications (PDF) Panfilio, K. A., Jentzsch, I. M. V., Benoit, J. B., Erezyilmaz, D., Suzuki, Y., Colella, S., ... & Weirauch, M. T. (2017). Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. bioRxiv, 201731. BJ Matthews, O Dudchenko, S Kingan, S Koren, I Antoshechkin Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control bioRxiv, 240747 McKenna, D. D., Scully, E. D., Pauchet, Y., Hoover, K., Kirsch, R., Geib, S. M., ... & Benoit, J. B. (2016). Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface. Genome biology, 17(1), 227. Poynton, H. C., Hasenbein, S., Benoit, J. B., Sepulveda, M. S., Poelchau, M. F., Hughes, D. S., ... & Werren, J. H. (2018). The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. Environmental science & technology, 52(10), 6009-6022. Hjelmen, C. E., J. S. Johnston. 2018. A phylogenetic analysis of genome size in male Sophophora: investigatons into sex differences in genome size. Submitted to J. Heredity 2/11/17. Dora Henriques1,2, Andreas Wallberg3, Julio Chávez-Galarza1,4, J. Spencer Johnston5, 4 Matthew T. Webster3, M. Alice Pinto1* 1918. Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula. Scientific Reports. 8:8552 | DOI:10.1038/s41598-018-26932-1 Silva AA, Braga LS, Corrêa AS, Holmes VR, Johnston JS, Oppert B, Guedes RNC, Tavares MG. 2018. Comparative cytogenetics and derived phylogenic relationship among Sitophilus grain weevils (Coleoptera, Curculionidae, Dryophthorinae). Comparative Cytogenetics 12: 223. Hjelmen CE, Johnston JS. 2017. The mode and tempo of genome size evolution in the subgenus Sophophora. PloS one 12: e0173505. Lower SS, Johnston JS, Stanger-Hall KF, Hjelmen CE, Hanrahan SJ, Korunes K, Hall D. 2017. Genome size in North American fireflies: substantial variation likely driven by neutral processes. Genome biology and evolution 9: 1499-1512. Muñoz I, Henriques D, Jara L, Johnston JS, Chávez‐Galarza J, De La Rúa P, Pinto MA. 2017. SNP s selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera). Molecular Ecology Resources 17: 783-795. Wenger JA, Cassone BJ, Legeai F, Johnston JS, Bansal R, Yates AD, Coates BS, Pavinato VA, Michel A. 2017. Whole genome sequence of the soybean aphid, Aphis glycines. Insect biochemistry and molecular biology. Johnston JS, Fiston-Lavier A-S, Teets NM, Denlinger DL, Peyton JT, Bustamante CD, Lee RE, Kelley JL, Muh-Ching Y. 2016. Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Rangel J, Baum K, Rubink WL, Coulson RN, Johnston JS, Traver BE. 2016a. Prevalence of Nosema species in a feral honey bee population: a 20-year survey. Apidologie 47: 561-571. Rangel J, Giresi M, Pinto MA, Baum KA, Rubink WL, Coulson RN, Johnston JS. 2016b. Africanization of a feral honey bee (Apis mellifera) population in South Texas: does a decade make a difference? Ecology and evolution 6: 2158-2169. Benoit, J. B., Adelman, Z. N., Reinhardt, K., Dolan, A., Poelchau, M., Jennings, E. C., ... & Zhu, F. (2016). Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nature communications, 7, ncomms10165. Arnqvist G, Sayadi A, Immonen E, Hotzy C, Rankin D, Tuda M, Hjelmen CE, Johnston JS. 2015. Genome size correlates with reproductive fitness in seed beetles. Proc R Soc B 282: 20151421. Chávez‐Galarza J, Henriques D, Johnston JS, Carneiro M, Rufino J, Patton JC, Pinto MA. 2015. Revisiting the Iberian honey bee (Apis mellifera iberiensis) contact zone: maternal and genome‐wide nuclear variations provide support for secondary contact from historical refugia. Molecular ecology 24: 2973-2992. Kapheim, K. M., Pan, H., Li, C., Salzberg, S. L., Puiu, D., Magoc, T., ... & Hernandez, A. (2015). Genomic signatures of evolutionary transitions from solitary to group living. Science, aaa4788. Cheng W, Lei J, Fox CW, Johnston JS, Zhu-Salzman K. 2015. Comparison of life history and genetic properties of cowpea bruchid strains and their response to hypoxia. Journal of insect physiology 75: 5-11. Muñoz I, Henriques D, Johnston JS, Chávez-Galarza J, Kryger P, Pinto MA. 2015. Reduced SNP panels for genetic identification and introgression analysis in the dark honey bee (Apis mellifera mellifera). PloS one 10: e0124365. Pinto MA, Chavez-Galarza J, Henriques D, Rufino J, Azevedo J, Johnston JS. 2015. Spatial patterns of single nucleotide polymorphisms (SNPs) support a scenario of secondary contact in Iberian honey bees (Apis mellifera iberiensis). In IUFRO Landscape Ecology Working Group International Conference. Rangel J, Strauss K, Seedorf K, Hjelmen CE, Johnston JS. 2015. Endopolyploidy changes with age- related polyethism in the honey bee, Apis mellifera. PloS one 10: e0122208. Azizi T, Johnston JS, Vinson SB. 2014. A gene involved in postmating flight muscle degeneration in red imported fire ant (Hymenoptera: Formicidae) queens. Annals of the Entomological Society of America 100: 270-274. Boussau B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston JS, Holland PW. 2014. Strepsiptera, phylogenomics and the long branch attraction problem. PLoS One 9: e107709. Chávez-Galarza J, Henriques D, Johnston JS, Rufino J, Pinto MA. 2014a. Análisis de introgresión en Apis mellifera iberiensis y Apis mellifera mellifera usando polimorfismos de nucleótidos simples (SNPs). In III Congresso Ibérico de Apicultura. Chávez-Galarza J, Henriques D, Johnston JS, Rufino J, Pinto MA. 2014b. Identificando genes que favorecen la adaptación local en Apis mellifera iberiensis. In III Congresso Ibérico de Apicultura: Livro de Resumos, pp. 56-56. Instituto Politécnico de Bragança. Ellis LL, Huang W, Quinn AM, Ahuja A, Alfrejd B, Gomez FE, Hjelmen CE, Moore KL, Mackay TF, Johnston JS. 2014. Intrapopulation genome size variation in D. melanogaster reflects life history variation and plasticity. PLoS genetics 10: e1004522. Kelley JL, Peyton JT, Fiston-Lavier A-S, Teets NM, Yee M-C, Johnston JS, Bustamante CD, Lee RE, Denlinger DL. 2014. Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. Nature communications 5: 4611. Pimsler ML, Pape T, Johnston JS, Wharton RA, Parrott JJ, Restuccia D, Sanford MR, Tomberlin JK, Tarone AM. 2014. Structural and genetic investigation of the egg and first-instar larva of an egg-laying population of Blaesoxipha plinthopyga (Diptera: Sarcophagidae), a species of forensic importance. Journal of medical entomology 51: 1283-1295. Pinto MA, Johnston JS, Rubink WL, Coulson RN, Patton JC, Sheppard WS. 2014a. Identification of Africanized honey bee (Hymenoptera: Apidae) mitochondrial DNA: validation of a rapid polymerase chain reaction-based assay. Annals of the Entomological Society of America 96: 679-684. Pinto MA, Sheppard WS, Johnston JS, Rubink WL, Coulson RN, Schiff NM, Kandemir I, Patton JC. 2014b. Honey bees (Hymenoptera: Apidae) of African origin exist in non-Africanized areas of the Southern United States: evidence from mitochondrial DNA. Annals of the Entomological Society of America 100: 289-295. Portnoy D, Hollenbeck C, Johnston J, Casman H, Gold J. 2014. Parthenogenesis in a whitetip reef shark Triaenodon obesus involves a reduction in ploidy. Journal of Fish Biology 85: 502-508. Scholes D, Suarez A, Smith A, Johnston S, Paige K. 2014. Organ-specific patterns of endopolyploidy in the giant ant Dinoponera australis. Journal of Hymenoptera Research 37: 113. Soria-Carrasco V, Gompert Z, Comeault AA, Farkas TE, Parchman TL, Johnston JS, Buerkle CA, Feder JL, Bast J, Schwander T. 2014a. Stick insect genomes reveal natural selection’s role in parallel speciation. Science 344: 738-742. Huang, W., Massouras, A., Inoue, Y., Peiffer, J., Ràmia, M., Tarone, A., ... & Magwire, M. (2014). Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome research, gr-171546. Soria-Carrasco V, Gompert Z, Comeault AA, Farkas TE, Parchman TL, Johnston JS, Buerkle CA, Feder JL, Bast J, Schwander T. 2014b. Data from: Stick insect genomes reveal natural selection's role in parallel speciation. Tarone AM, Tomberlin JK, Johnston JS, Wallace JR, Benbow ME, Mohr R, Mondor EB, Vanlaerhoven SL. 2014. Reply: A Correspondence from a maturing discipline. Journal of medical entomology 51: 490- 492. Pinto, M. A., Henriques, D., Chávez-Galarza, J., Kryger, P., Garnery, L., van der Zee, R., ... & Carreck, N. L. (2014). Genetic integrity of the Dark European honey bee (Apis mellifera mellifera) from protected populations: a genome-wide assessment using SNPs and mtDNA sequence data. Journal of Apicultural Research, 53(2), 269-278. Chavez-Galarza J, Henriques D, Johnston JS, Rufino J, Pinto MA. 2013b. Genome-wide scans detected signatures of selection in genes related with vision, xenobiotic metabolism, and immunity in the Iberian honey bee genome. In 43º International Apicultural Congress Apimondia. Chávez‐Galarza J, Henriques D, Johnston JS, Azevedo JC, Patton JC, Muñoz I, De la Rúa P, Pinto MA. 2013. Signatures of selection in the I berian honey bee (Apis mellifera iberiensis) revealed by a genome scan analysis of single nucleotide polymorphisms. Molecular
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