Population genomics of the yellow crazy ant and its intracellular microorganisms

Chapter 1

1. Bertelsmeier, C.; Ollier, S.; Liebhold, A.; Keller, L. Recent human history governs global ant invasion dynamics. Nat. Ecol. Evol. 2017, 1, 0184.

2. Abbott, K.L. Supercolonies of the invasive yellow crazy ant, Anoplolepis gracilipes, on an oceanic island: forager activity patterns, density and biomass. Insectes Sociaux 2005, 52, 266-273.

3. Thomas, M.L.; Tsutsui, N.D.; Holway, D.A. Intraspecific competition influences the symmetry and intensity of aggression in the Argentine ant. Behav. Ecol. 2005, 16, 472-481.

4. Cooling, M.; Hoffmann, B.D. Here today, gone tomorrow: declines and local extinctions of invasive ant populations in the absence of intervention. Biol. Invasions 2015, 17, 3351-3357.

5. Holway, D.A.; Suarez, A.V.; Case, T.J. Role of abiotic factors in governing susceptibility to invasion: a test with Argentine ants. Ecology 2002, 83, 1610-1619.

6. Bertelsmeier, C.; Keller, L. Bridgehead effects and role of adaptive evolution in invasive populations. Trends Ecol. Evol. 2018, 33, 527-534.

7. Wetterer, J.K. Worldwide distribution and potential spread of the long-legged ant, Anoplolepis gracilipes (Hymenoptera: Formicidae). Sociobiology 2005, 45, 77-97.

8. Ito, F.; Asfiya, W.; Kojima, J.I. Discovery of independent-founding solitary queens in the yellow crazy ant Anoplolepis gracilipes in East Java, Indonesia (Hymenoptera: Formicidae). Entomol. Sci. 2016, 19, 312-314.

9. Drescher, J.; Blüthgen, N.; Schmitt, T.; Bühler, J.; Feldhaar, H. Societies drifting apart? Behavioural, genetic and chemical differentiation between supercolonies in the yellow crazy ant Anoplolepis gracilipes. PLoS ONE 2010, 5, e13581.

10. Thomas, M.L.; Becker, K.; Abbott, K.; Feldhaar, H. Supercolony mosaics: two different invasions by the yellow crazy ant, Anoplolepis gracilipes, on Christmas Island, Indian Ocean. Biol. Invasions 2010, 12, 677-687.

11. Gruber, M.A.; Hoffmann, B.D.; Ritchie, P.A.; Lester, P.J. Recent behavioural and population genetic divergence of an invasive ant in a novel environment. Divers. Distrib. 2012, 18, 323-333.

12. Drescher, J.; Blüthgen, N.; Feldhaar, H. Population structure and intraspecific aggression in the invasive ant species Anoplolepis gracilipes in Malaysian Borneo. Mol. Ecol. 2007, 16, 1453-1465.

13. Werren, J.H.; Baldo, L.; Clark, M.E. Wolbachia: Master manipulators of invertebrate biology. Nat. Rev. Microbiol. 2008, 6, 741–751.

14. Zug, R.; Hammerstein, P. Bad guys turned nice? A critical assessment of Wolbachia mutualisms in arthropod hosts. Biol. Rev. 2015, 90, 89–111.

15. Pontieri, L.; Schmidt, A.M.; Singh, R.; Pedersen, J.S.; Linksvayer, T.A. Artificial selection on ant female caste ratio uncovers a link between female-biased sex ratios and infection by Wolbachia endosymbionts. J. Evol. Biol. 2017, 30, 225–234.

16. Tseng, S.P.; Hsu, P.W.; Lee, C.C.; Wetterer, J.K.; Hugel, S.; Wu, L.H.; Lee, C.Y.; Yoshimura, T.; Yang, C.C.S. Evidence for common horizontal transmission of Wolbachia among ants and ant crickets: Kleptoparasitism added to the list. Microorganisms 2020, 8, 805.

17. Sebastien, A.; Gruber, M.A.M.; Lester, P.J. Prevalence and genetic diversity of three bacterial endosymbionts (Wolbachia, Arsenophonus, and Rhizobiales) associated with the invasive yellow crazy ant (Anoplolepis gracilipes). Insectes Soc. 2012, 59, 33–40.

18. Young, H.S.; Parker, I.M.; Gilbert, G.S.; Guerra, A.S.; Nunn, C.L. Introduced species, disease ecology, and biodiversity–disease relationships. Trends Ecol. Evol. 2017, 32, 41-54.

19. Collins, L. M.; Warnock, N. D.; Tosh, D. G.; McInnes, C.; Everest, D.; Montgomery, W. I.; ...; Reid, N. Squirrelpox virus: assessing prevalence, transmission and environmental degradation. PLoS One 2014, 9, e89521.

20. Valles, S.M.; Varone, L.; Ramírez, L.; Briano, J. Multiplex detection of Solenopsis invicta viruses-1,-2, and-3. J. Virol. Methods 2009, 162, 276-279.

21. Sébastien, A.; Lester, P.J.; Hall, R.J.; Wang, J.; Moore, N.E.; Gruber, M.A. Invasive ants carry novel viruses in their new range and form reservoirs for a honeybee pathogen. Biol. Lett. 2015, 11, 20150610.

22. Yang, C.C.; Yu, Y.C.; Valles, S.M.; Oi, D.H.; Chen, Y.C.; Shoemaker, D.; Wu, W.J.; Shih, C.J. Loss of microbial (pathogen) infections associated with recent invasions of the red imported fire ant Solenopsis invicta. Biol. Invasions 2010, 12, 3307-3318.

23. Cremer, S. Pathogens and disease defense of invasive ants. Curr. Opin. Insect. Sci. 2019, 33, 63-68.

Chapter 2

1. O'Dowd D.J.; Green P.T.; Lake P.S. Invasional ‘meltdown’on an oceanic island. Ecol. Lett. 2003, 6:812-817.

2. Hoffmann B.D.; Hagedorn H. Quantification of supercolonial traits in the yellow crazy ant, Anoplolepis gracilipes. J. Insect Sci. 2014, 14,25.

3. Ito F.; Asfiya W.; Kojima Ji. Discovery of independent-founding solitary queens in the yellow crazy ant Anoplolepis gracilipes in east Java, Indonesia (Hymenoptera: Formicidae). Entomol. Sci. 2016, 19,312-314.

4. Gruber M.A.; Hoffmann B.D.; Ritchie P.A.; Lester P.J. Recent behavioural and population genetic divergence of an invasive ant in a novel environment. Divers. Distrib. 2012, 18,323-333.

5. Thomas, M.L.; Becker, K.; Abbott, K.; Feldhaar, H. Supercolony mosaics: two different invasions by the yellow crazy ant, Anoplolepis gracilipes, on Christmas Island, Indian Ocean. Biol. Invasions 2010, 12, 677-687.

6. Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30, 2114-2120.

7. Dierckxsens N.; Mardulyn P.; Smits G. Novoplasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 2016, 45,e18-e18.

8. Bernt M.; Donath A.; Jühling F.; Externbrink F.; Florentz C.; Fritzsch G.; Pütz J.; Middendorf M.; Stadler P.F. MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol. Phylogen. Evol. 2013, 69, 313-319.

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10. Laslett D.; Canbäck B. Arwen: A program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 2007, 24, 172-175.

11. Ronquist, F.; Huelsenbeck, J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19, 1572-1574.

12. Stamatakis A. Raxml version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014, 30,1312-1313.

13. Babbucci M.; Basso A.; Scupola A.; Patarnello T.; Negrisolo E. Is it an ant or a butterfly? Convergent evolution in the mitochondrial gene order of Hymenoptera and lepidoptera. Genome Biol. Evol. 2014, 6,3326-3343.

14. Yang S.; Li X.; Cai L-G; Qian Z-Q. Characterization of the complete mitochondrial genome of Formica selysi (Insecta: Hymenoptera: Formicidae: Formicinae). Mitochondr DNA Part A. 2016, 27,3378-3380.

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16. Liu J.-H.; Jia P.-F.; Fu J.-Q.; Dan W.-L.; Yang L.-Y.; Wang Q.-M.; Li Z.-N. Characterization of mitochondrial genome and phylogenetic implications for chinese black ant, Polyrhachis dives (Hymenoptera: Formicidae). Mitochondr DNA Part B 2017, 2,679-680.

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Chapter 3

1. Colautti, R.I.; Lau, J.A. Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation. Mol. Ecol. 2015, 24, 1999- 2017.

2. Bertelsmeier, C.; Ollier, S.; Liebhold, A.; Keller, L. Recent human history governs global ant invasion dynamics. Nat. Ecol. Evol. 2017, 1, 0184.

3. Abbott, K.L. Supercolonies of the invasive yellow crazy ant, Anoplolepis gracilipes, on an oceanic island: forager activity patterns, density and biomass. Insectes Sociaux 2005, 52, 266-273.

4. Thomas, M.L.; Tsutsui, N.D.; Holway, D.A. Intraspecific competition influences the symmetry and intensity of aggression in the Argentine ant. Behav. Ecol. 2005, 16, 472-481.

5. Privman, E.; Cohen, P.; Cohanim, A.B.; Riba-Grognuz, O.; Shoemaker, D.; Keller, L. Positive selection on sociobiological traits in invasive fire ants. Mol. Ecol. 2018, 27, 3116-3130.

6. Yang, C.C.; Yu, Y.C.; Valles, S.M.; Oi, D.H.; Chen, Y.C.; Shoemaker, D.; Wu, W.J.; Shih, C.J. Loss of microbial (pathogen) infections associated with recent invasions of the red imported fire ant Solenopsis invicta. Biol. Invasions 2010, 12, 3307-3318.

7. Rey, O.; Estoup, A.; Vonshak, M.; Loiseau, A.; Blanchet, S.; Calcaterra, L.; Chifflet, L.; Rossi, J.P.; Kergoat, G.J.; Foucaud, J.; Orivel, J. Where do adaptive shifts occur during invasion? A multidisciplinary approach to unravelling cold adaptation in a tropical ant species invading the Mediterranean area. Ecol. Lett. 2012, 15, 1266- 1275.

8. Foucaud, J.; Rey, O.; Robert, S.; Crespin, L.; Orivel, J.; Facon, B.; Loiseau, A.; Jourdan, H.; Kenne, M.; Masse, P.S.M.; Tindo, M. Thermotolerance adaptation to human-modified habitats occurs in the native range of the invasive ant Wasmannia auropunctata before long-distance dispersal. Evol. Appl. 2013, 6, 721- 734.

9. Estoup, A.; Ravigné, V.; Hufbauer, R.; Vitalis, R.; Gautier, M.; Facon, B. Is there a genetic paradox of biological invasion? Annu. Rev. Ecol. Evol. Syst. 2016, 47, 51-72.

10. Wetterer, J.K. Worldwide distribution and potential spread of the long-legged ant, Anoplolepis gracilipes (Hymenoptera: Formicidae). Sociobiology 2005, 45, 77-97.

11. Ito, F.; Asfiya, W.; Kojima, J.I. Discovery of independent-founding solitary queens in the yellow crazy ant Anoplolepis gracilipes in East Java, Indonesia (Hymenoptera: Formicidae). Entomol. Sci. 2016, 19, 312-314.

12. O'Dowd, D.J.; Green, P.T.; Lake, P.S. Invasional ‘meltdown’on an oceanic island. Ecology Lett. 2003, 6, 812-817.

13. Cooling, M.; Hoffmann, B.D. Here today, gone tomorrow: declines and local extinctions of invasive ant populations in the absence of intervention. Biol. Invasions 2015, 17, 3351-3357.

14. Drescher, J.; Blüthgen, N.; Feldhaar, H. Population structure and intraspecific aggression in the invasive ant species Anoplolepis gracilipes in Malaysian Borneo. Mol. Ecol. 2007, 16, 1453-1465.

15. Drescher, J.; Blüthgen, N.; Schmitt, T.; Bühler, J.; Feldhaar, H. Societies drifting apart? Behavioural, genetic and chemical differentiation between supercolonies in the yellow crazy ant Anoplolepis gracilipes. PLoS ONE 2010, 5, e13581.

16. Thomas, M.L.; Becker, K.; Abbott, K.; Feldhaar, H. Supercolony mosaics: two different invasions by the yellow crazy ant, Anoplolepis gracilipes, on Christmas Island, Indian Ocean. Biol. Invasions 2010, 12, 677-687.

17. Gruber, M.A.; Hoffmann, B.D.; Ritchie, P.A.; Lester, P.J. Recent behavioural and population genetic divergence of an invasive ant in a novel environment. Divers. Distrib. 2012, 18, 323-333.

18. Peterson, B.K.; Weber, J.N.; Kay, E.H.; Fisher, H.S.; Hoekstra, H.E. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 2012, 7, e37135.

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Chapter 4

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2. Zug, R.; Hammerstein, P. Bad guys turned nice? A critical assessment of Wolbachia mutualisms in arthropod hosts. Biol. Rev. 2015, 90, 89–111.

3. Landmann, F.; Foster, J.M.; Michalski, M.L.; Slatko, B.E.; Sullivan, W. Co- evolution between an endosymbiont and its nematode host: Wolbachia asymmetric posterior localization and AP polarity establishment. PLoS Negl. Trop. Dis. 2014, 8, e3096.

4. Lefoulon, E.; Bain, O.; Makepeace, B.L.; d’Haese, C.; Uni, S.; Martin, C.; Gavotte, L. Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts. PeerJ 2016, 4, e1840.

5. Balvín, O.; Roth, S.; Talbot, B.; Reinhardt, K. Co-speciation in bedbug Wolbachia parallel the pattern in nematode hosts. Sci. Rep. 2018, 8, 8797.

6. Newton, I.L.; Rice, D.W. The Jekyll and Hyde symbiont: Could Wolbachia be a nutritional mutualist? J. Bacteriol. 2020, 202, e00589-19.

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9. Schuler, H.; Köppler, K.; Daxböck-Horvath, S.; Rasool, B.; Krumböck, S.; Schwarz, D.; Hoffmeister, T.S.; Schlick-Steiner, B.C.; Steiner, F.M.; Telschow, A.; et al. The hitchhiker’s guide to Europe: The infection dynamics of an ongoing Wolbachia invasion and mitochondrial selective sweep in Rhagoletis cerasi. Mol. Ecol. 2016, 25, 1595–1609.

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12. Pontieri, L.; Schmidt, A.M.; Singh, R.; Pedersen, J.S.; Linksvayer, T.A. Artificial selection on ant female caste ratio uncovers a link between female-biased sex ratios and infection by Wolbachia endosymbionts. J. Evol. Biol. 2017, 30, 225–234.

13. Ün, Ç.; Schultner, E.; Manzano-Marín, A.; Flórez, L.V.; Seifert, B.; Heinze, J.; Oettler, J. Cytoplasmic incompatibility between Old and New World populations of a tramp ant. bioRxiv doi: 10.1101/2020.03.13.988675

14. Wetterer, J.K. Worldwide distribution and potential spread of the long-legged ant, Anoplolepis gracilipes (Hymenoptera: Formicidae). Sociobiology 2005, 45, 77–97.

15. Ito, F.; Asfiya, W.; Kojima, J.I. Discovery of independent-founding solitary queens in the yellow crazy ant Anoplolepis gracilipes in East Java, Indonesia (Hymenoptera: Formicidae). Entomol. Sci. 2016, 19, 312–314.

16. Drescher, J.; Blüthgen, N.; Schmitt, T.; Bühler, J.; Feldhaar, H. Societies drifting apart? Behavioural, genetic and chemical differentiation between supercolonies in the yellow crazy ant Anoplolepis gracilipes. PLoS ONE 2010, 5, e13581.

17. Gruber, M.A.; Hoffmann, B.D.; Ritchie, P.A.; Lester, P.J. Recent behavioural and population genetic divergence of an invasive ant in a novel environment. Divers. Distrib. 2012, 18, 323–333.

18. Tseng, S.P.; Hsu, P.W.; Lee, C.C.; Wetterer, J.K.; Hugel, S.; Wu, L.H.; Lee, C.Y.; Yoshimura, T.; Yang, C.C.S. Evidence for common horizontal transmission of Wolbachia among ants and ant crickets: Kleptoparasitism added to the list. Microorganisms 2020, 8, 805.

19. Sebastien, A.; Gruber, M.A.M.; Lester, P.J. Prevalence and genetic diversity of three bacterial endosymbionts (Wolbachia, Arsenophonus, and Rhizobiales) associated with the invasive yellow crazy ant (Anoplolepis gracilipes). Insectes Soc. 2012, 59, 33–40.

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Chapter 5

1. Valles S.M.; Chen Y.; Firth A.E.; Guérin D.M.; Hashimoto Y.; Herrero S.; de Miranda J.R.; Ryabov E. ICTV Virus Taxonomy Profile: Dicistroviridae. J. Gen. Virol. 2017, 98,355-356.

2. Kleanthous E.; Olendraite I.; Lukhovitskaya N.I.; Firth A.E. Discovery of three RNA viruses using ant transcriptomic datasets. Arch. Virol. 2019, 164,643-647.

3. Valles S.M.; Rivers A.R. Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range. Virus Genes 2019, 55,368-380.

4. Viljakainen L.; Holmberg I.; Abril S.; Jurvansuu J. Viruses of invasive Argentine ants from the European Main supercolony: Characterization, interactions and evolution. J. Gen. Virol. 2018, 25,1129-40.

5. Reuter G.; Pankovics P.; Gyöngyi Z., Delwart E.; Boros Á. Novel dicistrovirus from bat guano. Arch. Virol. 2014, 159,3453-6.

6. Shi M.; Lin X.D.; Tian J.H.; Chen L.J.; Chen X.; Li C.X.; Qin X.C.; Li J.; Cao J.P.; Eden J.S.; Buchmann J. Redefining the invertebrate RNA virosphere. Nature 2016, 540, 539-43.

7. Mihara T.; Nishimura Y.; Shimizu Y.; Nishiyama H.; Yoshikawa G.; Uehara H.; Hingamp P.; Goto S.; Ogata H. Linking virus genomes with host taxonomy. Viruses 2016, 8, 66.

8. Payne A.N.; Shepherd T.F.; Rangel J. The detection of honey bee (Apis mellifera) associated viruses in ants. Sci. Rep. 2020, 10,2923.

9. Cooling M.; Gruber M.A.M.; Hoffmann B.D.; Sébastien A.; Lester P.J. A metatranscriptomic survey of the invasive yellow crazy ant, Anoplolepis gracilipes, identifies several potential viral and bacterial pathogens and mutualists. Insect Soc. 2017, 64, 197-207.

10. Bolger A.M.; Lohse M.; Usadel B. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics 2014, 30, 2114-2120.

11. Grabherr M.G.; Haas B.J.; Yassour M.; Levin J.Z.; Thompson D.A.; Amit I.; Adiconis X.; Fan L.; Raychowdhury R.; Zeng Q.; Chen Z.; Mauceli E.; Hacohen N.; Gnirke A.; Rhind N.; di Palma F.; Birren B.W.; Nusbaum C.; Lindblad-Toh K.; Friedman N.; Regev A. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011, 29,644-652.

12. Buchfink B.; Xie C.; Huson D.H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 2015, 12, 59.

13. Huson D.; Beier S.; Flade I.; Gorska A.; El-Hadidi M.; Mitra S.; Ruscheweyh H.; Rewati Tappu D. MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 2016, 12, e1004957.

14. Rombel I.T.; Sykes K.F.; Rayner S.; Johnston S.A. ORF-FINDER: a vector for high- throughput gene identification. Gene 2002, 282, 33-41.

15. Marchler-Bauer A.; Derbyshire M.K.; Gonzales N.R.; Lu S.; Chitsaz F.; Geer L.Y.; Geer R.C.; He J.; Gwadz M.; Hurwitz D.I.; Lanczycki C.J.; Lu F.; Marchler G.H.; Song J.S.; Thanki N.; Wang Z.; Yamashita R.A.; Zhang D.; Zheng C.; Bryant S.H. CDD: NCBI's conserved domain database. Nucleic Acids Res. 2015, 43, D222-D226.

16. Darriba D.; Posada D.; Kozlov A.M.; Stamatakis A.; Morel B.; Flouri T. ModelTest- NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol. Biol. Evol. 2020, 37,291-294.

17. Kozlov A.M.; Darriba D.; Flouri T.; Morel B.; Stamatakis A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 2019, 35, 4453-4455.

18. Letunic I.; Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019, 47, W256-W259.

19. Yang C.C.; Yu Y.C.; Valles S.M.; Oi D.H.; Chen Y.C.; Shoemaker D.W.; Wu W.J.; Shih C.J. Loss of microbial (pathogen) infections associated with recent invasions of the red imported fire ant Solenopsis invicta. Biol. Invasions 2010, 3, 333- 345.

20. Culley A.I.L.; Suttle C.A. Family dicistroviridae. In: King AMQA, Carstens EB, Lefkowitz EJ (eds) Virus Taxonomy, Classification and Nomenclature of Viruses. 9th Report of the ICTV Elsevier Academic Press, Amsterdam, 2012, pp 840-854.

Chapter 6

1. Olendraite, I.; Lukhovitskaya, N.I.; Porter, S.D.; Valles, S.M.; Firth, A.E. Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses. J. Gen. Virol. 2017, 98, 2368.

2. Olendraite, I.; Brown, K.; Valles, S.M.; Firth, A.E.; Chen, Y.; Guérin, D.M.; Hashimoto, Y.; Herrero, S.; de Miranda, J.R.; Ryabov, E.; Consortium, I.R. ICTV virus taxonomy profile: Polycipiviridae. J. Gen. Virol. 2019, 100, 554.

3. Valles, S.M.; Strong, C.A.; Hashimoto, Y. A new positive-strand RNA virus with unique genome characteristics from the red imported fire ant, Solenopsis invicta. Virology 2007, 365, 457-463.

4. Viljakainen, L.; Holmberg, I.; Abril, S.; Jurvansuu, J. Viruses of invasive Argentine ants from the European main supercolony: characterization, interactions and evolution. J. Gen. Virol. 2018, 99, 1129-1140.

5. Shi, M.; Lin, X.D.; Tian, J.H.; Chen, L.J.; Chen, X.; Li, C.X.; Qin, X.C.; Li, J.; Cao, J.P.; Eden, J.S.; Buchmann, J. Redefining the invertebrate RNA virosphere. Nature 2016, 540, 539-543.

6. Valles, S.M.; Rivers, A.R. Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range. Virus Genes 2019, 55, 368-380.

7. Temmam, S.; Hul, V.; Bigot, T.; Hoem, T.; Gorman, C.; Duong, V.; Dussart, P.; Cappelle, J.; Eloit, M. A novel Polycipiviridae virus identified in Pteropus lylei stools. Microbiol. Resour. Announc. 2019, 8, e01662-18.

8. Sanborn, M.A.; Klein, T.A.; Kim, H.C.; Fung, C.K.; Figueroa, K.L.; Yang, Y.; Asafo- Adjei, E.A.; Jarman, R.G.; Hang, J. Metagenomic analysis reveals three novel and prevalent mosquito viruses from a single pool of Aedes vexans nipponii Collected in the Republic of Korea. Viruses 2019, 11, 222.

9. Fukasawa, F.; Hirai, M.; Takaki, Y.; Shimane, Y.; Thomas, C.E.; Urayama, S.I.; Nunoura, T.; Koyama, S. A new polycipivirus identified in Colobopsis shohki. Arch. Virol. 2020, 165, 761-763.

10. Wright, A.A.; Cross, A.R.; Harper, S.J. A bushel of viruses: Identification of seventeen novel putative viruses by RNA-seq in six apple trees. PLoS One 2020, 15, e0227669.

11. Manfredini, F.; Shoemaker, D.; Grozinger, C.M. Dynamic changes in host–virus interactions associated with colony founding and social environment in fire ant queens (Solenopsis invicta). Ecol. Evol. 2016, 6, 233-244.

12. Lauring, A.S.; Andino, R. Quasispecies theory and the behavior of RNA viruses. PLoS Pathog. 2010, 6, e1001005.

13. Lee, C.C.; Lin, C.Y.; Hsu, H.W.; Yang, C.C.S. Complete genome sequences of two novel dicistroviruses detected in the yellow crazy ant, Anoplolepis gracilipes Arch. Vriol. (in press).

14. Cooling, M.; Gruber, M.A.M.; Hoffmann, B.D.; Sébastien, A.; Lester, P.J. A metatranscriptomic survey of the invasive yellow crazy ant, Anoplolepis gracilipes, identifies several potential viral and bacterial pathogens and mutualists. Insectes Soc. 2017, 64, 197-207.

15. Bolger, A.M.; Lohse, M.; Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014, 30, 2114-2120.

16. Grabherr, M.G.; Haas, B.J.; Yassour, M.; Levin, J.Z.; Thompson, D.A.; Amit, I.; Adiconis, X.; Fan, L.; Raychowdhury, R.; Zeng, Q.; Chen, Z. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29, 644-652.

17. Buchfink, B.; Xie, C.; Huson, D.H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 2015, 12, 59-60.

18. Huson, D.H.; Beier, S.; Flade, I.; Górska, A.; El-Hadidi, M.; Mitra, S.; Ruscheweyh, H.J.; Tappu, R. MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 2016, 12, e1004957.

19. Rombel I.T.; Sykes K.F.; Rayner S.; Johnston S.A. ORF-FINDER: a vector for high- throughput gene identification. Gene 2002, 282, 33-41.

20. Söding, J.; Biegert, A.; Lupas, A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005, 33, W244- W248.

21. Finn, R.D.; Coggill, P.; Eberhardt, R.Y.; Eddy, S.R.; Mistry, J.; Mitchell, A.L.; Potter, S.C.; Punta, M.; Qureshi, M.; Sangrador-Vegas, A.; Salazar, G.A. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016, 44, D279-D285.

22. Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The protein data bank. Nucleic Acids Res. 2000, 28, 235-242.

23. Untergasser, A.; Cutcutache, I.; Koressaar, T.; Ye, J.; Faircloth, B.C.; Remm, M.; Rozen, S.G. Primer3—new capabilities and interfaces. Nucleic Acids Res. 2012, 40, e115-e115.

24. Kumar, S.; Stecher, G.; Tamura, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 2016, 33, 1870-1874.

25. Darriba, D.; Posada, D.; Kozlov, A.M.; Stamatakis, A.; Morel, B.; Flouri, T. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol. Biol. Evol. 2020, 37, 291-294.

26. Kozlov, A.M.; Darriba, D.; Flouri, T.; Morel, B.; Stamatakis, A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 2019, 35, 4453-4455.

27. Ronquist, F.; Huelsenbeck, J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19, 1572-1574.

28. Letunic, I.; Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019, 47, W256-W259.

29. Darriba, D.; Taboada, G.L.; Doallo, R.; Posada, D. jModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 2012, 9, 772-772.

30. Xu, B.; Yang, Z. PAMLX: a graphical user interface for PAML. Mol. Biol. Evol. 2013, 30, 2723-2724.

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32. Hashimoto, Y.; Valles, S.M. Infection characteristics of Solenopsis invicta virus 2 in the red imported fire ant, Solenopsis invicta. J. Invertebr. Pathol. 2008, 99, 136- 140.

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