The evolution, diversity, and host associations of rhabdoviruses

Virus Evolution

Volumn 1, Issue 1, 2015, Pages

  Longdon, Ben ^a   Murray, Gemma G R ^a   Palmer, William J ^a   Day, Jonathan P ^a   Parker, Darren J ^b,c   Welch, John J ^a   Obbard, Darren J ^d   Jiggins, Francis M ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF ST ANDREWS   (United Kingdom)

^c UNIVERSITY OF JYVÄSKYLÄ   (Finland)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Arthropod; Host shift; Insect; Mononegavirales; Rhabdoviridae; Virus

Indexed keywords

EID: 85084326635     PISSN: None     EISSN: 20571577     Source Type: Journal    
DOI: 10.1093/ve/vev014     Document Type: Article

References (64)

1. Aguiar, E. R. et al. (2015) 'Sequence-Independent Characterization of Viruses Based on the Pattern of Viral Small RNAs Produced by the Host', Nucleic Acids Research, 43: 6191-206.
2. Ahne, W. et al. (2002) 'Spring Viremia of Carp (SVC)', Diseases of Aquatic Organisms, 52: 261-72.
3. Aiewsakun, P., and Katzourakis, A. (2015) 'Endogenous Viruses: Connecting Recent and Ancient Viral Evolution', Virology, 479-480C: 26-37.
4. Anisimova, M., and Gascuel, O. (2006) 'Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative', Systems Biology, 55: 539-52.
5. Aznar-Lopez, C. et al. (2013) 'Detection of Rhabdovirus Viral RNA in Oropharyngeal Swabs and Ectoparasites of Spanish Bats', Journal of General Virology, 94: 69-75.
6. Ballinger, M. J., Bruenn, J. A., and Taylor, D. J. (2012) 'Phylogeny, Integration and Expression of Sigma Virus-like Genes in Drosophila', Molecular Phylogenetics Evolution, 65: 251-8.
7. Bazinet, A., Myers, D., and Khatavkar, P. (2009) genealogicalSorting v.0.91.
8. Bhatia, G. et al. (2013) 'Estimating and Interpreting FST: The Impact of Rare Variants', Genome Research, 23: 1514-21.
9. Bootsma, R., Dekinkelin, P., and Leberre, M. (1975) 'Transmission Experiments with Pike Fry (Esox-Lucius L) Rhabdovirus', Journal of Fish Biology, 7: 269-76.
10. Bourhy, H. et al. (2005) 'Phylogenetic Relationships Among Rhabdoviruses Inferred Using the L Polymerase Gene', Journal of General Virology, 86: 2849-58.
11. Capella-Gutierrez, S., Silla-Martinez, J. M., and Gabaldon, T. (2009) 'trimAl: A Tool for Automated Alignment Trimming in Large-Scale Phylogenetic Analyses', Bioinformatics, 25: 1972-3.
12. Chiba, S. et al. (2011) 'Widespread Endogenization of Genome Sequences of Non-Retroviral RNA Viruses into Plant Genomes', Plos Pathogens, 7: e1002146.
13. Cummings, M. P., Neel, M. C., and Shaw, K. L. (2008) 'A Genealogical Approach to Quantifying Lineage Divergence', Evolution, 62: 2411-22.
14. Dietzgen, R. G., and Kuzmin, I. V. (2012) Rhabdoviruses: Molecular Taxonomy, Evolution, Genomics, Ecology, Host-Vector Interactions, Cytopathology and Control. Norfolk, UK: Caister Academic Press.
15. Dorson, M. et al. (1987) 'Susceptibility of Pike (Esox-Lucius) to Different Salmonid Viruses (Ipn, Vhs, Ihn) and to the Perch Rhabdovirus', Bulletin Francais De La Peche Et De La Pisciculture, 307: 91-101.
16. Drummond, A. J. et al. (2006) 'Relaxed Phylogenetics and Dating with Confidence', PLoS Biology, 4: e88.
17. Drummond, A. J. et al. (2012) 'Bayesian Phylogenetics with BEAUti and the BEAST 1.7', Molecular Biology and Evolution, 29: 1969-73.
18. Dudas, G., and Obbard, D. J. (2015) 'Are Arthropods at the Heart of Virus Evolution?', eLife, 4: e06837.
19. Edwards, C. J. et al. (2011) 'Ancient Hybridization and An Irish Origin for the Modern Polar Bear Matriline', Current Biology, 21: 1251-8.
20. Faria, N. R. et al. (2013) 'Simultaneously Reconstructing Viral Cross-Species Transmission History and Identifying the Underlying Constraints', Philosophical Transactions of the Royal Society of London B Biological Sciences, 368: 20120196.
21. Fort, P. et al. (2011) 'Fossil Rhabdoviral Sequences Integrated into Arthropod Genomes: Ontogeny, Evolution, and Potential Functionality', Molecular Biology and Evolution, 29: 381-90.
22. Guindon, S. et al. (2010) 'New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0', Systems Biology, 59: 307-21.
23. Haenen, O., and Davidse, A. (1993) 'Comparative Pathogenicity of Two Strains of Pike Fry Rhabdovirus and Spring Viremia of Carp Virus for Young Roach, Common Carp, Grass Carp and Rainbow Trout', Diseases of Aquatic Organisms, 15: 87-92.
24. Hampson, K. et al. (2015) 'Estimating the Global Burden of Endemic Canine Rabies', PLoS Neglected Tropical Diseases, 9: e0003709.
25. Hogenhout, S. A., Redinbaugh, M. G., and Ammar, E. D. (2003) 'Plant and Animal Rhabdovirus Host Range: A Bug's View', Trends in Microbiology, 11: 264-71.
26. Hommola, K. et al. (2009) 'A Permutation Test of Host-Parasite Cospeciation', Molecuar Biology and Evolution, 26: 1457-68.
27. Hudson, R. R., Slatkin, M., and Maddison, W. P. (1992) 'Estimation of Levels of Gene Flow from DNA Sequence Data', Genetics, 132: 583-9.
28. Jeyaprakash, A., and Hoy, M. A. (2009) 'First Divergence Time Estimate of Spiders, Scorpions, Mites and Ticks (Subphylum: Chelicerata) Inferred from Mitochondrial Phylogeny', Experimental and Applied Acarology, 47: 1-18.
29. Katoh, K., and Standley, D. M. (2013) 'MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability', Molecular Biology and Evolution, 30: 772-80.
30. Katzourakis, A., and Gifford, R. J. (2010) 'Endogenous Viral Elements in Animal Genomes', Plos Genetics, 6: e1001191.
31. L'Heritier, P. H., and Teissier, G. (1937) 'Une Anomalie Physiologique Héréditaire Chez la Drosophile', Comptes Rendus de l'Academie des Sciences Paris, 231: 192-4.
32. Le, S. Q., and Gascuel, O. (2008) 'An Improved General Amino Acid Replacement Matrix', Molecular Biology and Evolution, 25: 1307-20.
33. Lemey, P. et al. (2014) 'Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2', PLoS Pathogens, 10: e1003932.
34. Li, C. X. et al. (2015) 'Unprecedented Genomic Diversity of RNA Viruses in Arthropods Reveals the Ancestry of Negative-Sense RNA Viruses', eLife, 10.7554/eLife.05378.
35. Lipkin, W. I., and Anthony, S. J. (2015) 'Virus Hunting', Virology, 479-480C: 194-9.
36. Liu, S., Vijayendran, D., and Bonning, B. C. (2011) 'Next Generation Sequencing Technologies for Insect Virus Discovery', Viruses, 3: 1849-69.
37. Longdon, B., and Jiggins, F. M. (2012) 'Vertically Transmitted Viral Endosymbionts of Insects: Do Sigma Viruses Walk Alone?', Proceedings of the Biological Sciences, 279: 3889-98.
38. Longdon, B., and Jiggins, F. M. (2011) ICTV sigmavirus species and genus proposal. http://ictvonline.org/proposals/2011.007a-dV.A.v2. Sigmavirus.pdf .
39. Longdon, B., and Jiggins, F. M. (2010) 'Sigma Viruses from Three Species of Drosophila form a Major New Clade in the Rhabdovirus Phylogeny', Proceedings of the Royal Society B, 277: 35-44.
40. Longdon, B., and Jiggins, F. M. (2012) 'The Sigma Viruses of Drosophila', in Dietzgen, R., and Kuzmin, I. (eds.) Rhabdoviruses: Molecular Taxonomy, Evolution, Genomics, Ecology, Cytopathology and Control, pp. 117-132. Norfolk, UK: Caister Academic Press.
41. Longdon, B., and Jiggins, F. M. (2011) 'Host Phylogeny Determines Viral Persistence and Replication in Novel Hosts', PLoS Pathogens, 7: e1002260.
42. Longdon, B., and Jiggins, F. M. (2011) 'Host Switching by a Vertically-Transmitted Rhabdovirus in Drosophila', Biology Letters, 7: 747-50.
43. Longdon, B., and Jiggins, F. M. (2011) 'Rhabdoviruses in Two Species of Drosophila: Vertical Transmission and a Recent Sweep', Genetics, 188: 141-50.
44. Longdon, B., and Jiggins, F. M. (2014) 'The Evolution and Genetics of Virus Host Shifts', PLoS Pathogens, 10: e1004395.
45. Longdon, B., and Jiggins, F. M. (2015) 'The Causes and Consequences of Changes in Virulence following Pathogen Host Shifts', PLoS Pathogens, 11: e1004728.
46. Minin, V. N., and Suchard, M. A. (2008) 'Counting Labeled Transitions in Continuous-Time Markov Models of Evolution', Journal of Mathematical Biology, 56: 391-412.
47. Misof, B. et al. (2014) 'Phylogenomics Resolves the Timing and Pattern of Insect Evolution', Science, 346: 763-7.
48. Okland, A. L. et al. (2014) 'Genomic Characterization and Phylogenetic Position of Two New Species in Rhabdoviridae Infecting the Parasitic Copepod, Salmon Louse (Lepeophtheirus salmonis)', Plos One, 9: e112517.
49. Omland, K. E. (1999) 'The Assumptions and Challenges of Ancestral State Reconstructions', Systems Biology 48: 604-11.
50. Parker, D. J. et al. (2015) 'How Consistent are the Transcriptome Changes Associated with Cold Acclimation in Two Species of the Drosophila Virilis Group?', Heredity (Edinburgh), 115: 13-21.
51. Pfeilputzien, C. (1978) 'Experimental Transmission of Spring Viremia of Carp Through Carp Lice (Argulus-Foliaceus)', Zentralblatt Fur Veterinarmedizin Reihe B-Journal of Veterinary Medicine Series B-Infectious Diseases Immunology Food Hygiene Veterinary Public Health, 25: 319-23.
52. Rambaut, A. (2011) 'FigTree', (v1.3 ed). http://tree.bio.ed.ac.uk/software/figtree/ .
53. Rambaut, A., and Drummond, A. J. (2007) Tracer v1.6 http://beast.bio.ed.ac.uk/Tracer
54. Rosen, L. (1980) 'Carbon-dioxide Sensitivity in Mosquitos Infected with Sigma, Vesicular Stomatitis, and Other Rhabdoviruses', Science, 207: 989-91.
55. Shroyer, D. A., and Rosen, L. (1983) 'Extrachromosomal-Inheritance of Carbon-dioxide Sensitivity in the Mosquito Culex-Quinquefasciatus', Genetics, 104: 649-59.
56. Streicker, D. G. et al. (2010) 'Host Phylogeny Constrains Cross-Species Emergence and Establishment of Rabies Virus in Bats', Science, 329: 676-9.
57. Talavera, G., and Castresana, J. (2007) 'Improvement of Phylogenies After Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments', Systems Biology, 56: 564-77.
58. van Mierlo, J. T. et al. (2014) 'Novel Drosophila Viruses Encode Host-specific Suppressors of RNAi', PLoS Pathogens, 10: e1004256.
59. Walker, P. J., Blasdell, K. R., and Joubert, D. A. (2012) 'Ephemeroviruses: Athropod-borne Rhabdoviruses of Ruminants, with Large, Complex Genomes', in Dietzgen, R. G., and Kuzmin, I. V. (eds.) Rhabdoviruses: Molecular Taxonomy, Evolution, Genomics, Ecology, Host-Vector Interactions, Cytopathology and Control, pp. 59-88. Norfolk, UK: Caister Academic Press.
60. Walker, P. J., Blasdell, K. R., and Joubert, D. A. (2011) 'Rhabdovirus Accessory Genes', Virus Research, 162: 110-25.
61. Walker, P. J., Blasdell, K. R., and Joubert, D. A. (2015) 'Evolution of Genome Size and Complexity in the Rhabdoviridae', PLoS Pathogens, 11: e1004664.
62. Wang, Z., Gerstein, M., and Snyder, M. (2009) 'RNA-Seq: A Revolutionary Tool for Transcriptomics', Nature Review Genetics, 10: 57-63.
63. Webster, C. L. et al. (2015) 'The Discovery, Distribution and Evolution of Viruses Associated with Drosophila melanogaster. PLoS Biology, 13: e1002210.
64. Weinert, L. A. et al. (2012) 'Molecular Dating of Human-to-Bovid Host Jumps by Staphylococcus aureus Reveals an Association with the Spread of Domestication', Biology Letters, 8: 829-32.