The bean common mosaic virus lineage of potyviruses: Where did it arise and when?

Archives of Virology

Volumn 153, Issue 12, 2008, Pages 2177-2187

  Gibbs, A J ^b   Trueman, J W H ^a   Gibbs, M J ^b  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b NONE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION; GENETICS; LEGUME; MOLECULAR EVOLUTION; PHYLOGENY; PLANT DISEASE; POTYVIRUS; SHORT SURVEY; VIROLOGY;

EVOLUTION, MOLECULAR; FABACEAE; PHYLOGENY; PLANT DISEASES; POTYVIRUS;

BEAN COMMON MOSAIC VIRUS; POTYVIRUS;

EID: 58149326827     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-008-0256-x     Document Type: Short Survey

References (61)

1. MJ Adams JF Antoniw CM Fauquet 2005 Molecular criteria for genus and species discrimination within the family Potyviridae Arch Virol 150 459 479
2. Anon (2008) Phylogeography. http://en.wikipedia.org/wiki/ Phylogeography#cite_note-6
3. Bellwood P (2005) First farmers: the origins of agricultural societies. Blackwell Publishing, Oxford
4. Blackman RL, Eastop VF (2000) Aphids on the worlds crops an identification and information guide. Natural History Museum, London
5. W Bleeker A Franzke K Pollmann AHD Brown H Hurka 2002 Phylogeny and biogeography of southern hemisphere high-mountain Cardamine species (Brassicaceae) Aust Syst Bot 15 575 581
6. Brunt AA, Crabtree K, Dallwitz M, Gibbs A, Watson L (1996) Viruses of plants. CAB International, UK
7. Burkill IH (1966) A dictionary of the economic products of the Malay Peninsular. Ministryo Agriculture and Cooperatives, Kuala Lumpur
8. CVF Carrington JE Foster OG Pybus SN Bennett EC Holmes 2005 Invasion and maintenance of dengue virus type 2 and type 4 in the Americas J Virol 79 14680 14687
9. Carver M, Gross GF, Woodward TE (1991) Hemiptera (Bugs, leafhoppers, cicadas, aphids, scale insects, etc.). In: Naumann ID (ed) The insects of australia, vol 1. Melbourne University Press, Melbourne
10. M Chacon SB Pickersgill DG Debouck 2005 Domestication patterns in common bean (Phaseolus vulgaris L.) and the origin of the Mesoamerican and Andean cultivated races Theor Appl Genet 110 432 444
11. AJ Cockbain AJ Gibbs GD Heathcote 1963 Some factors affecting the transmission of sugar-beet mosaic and pea mosaic viruses by Aphis fabae and Myzus persicae Ann Appl Biol 52 133 143
12. Diamond J (1997) Guns, germs and steel: a short history of everybody for the past 13, 000 years. Random House, London
13. J Diamond P Bellwood 2003 Farmers and their languages: the first expansions Science 300 597 603
14. Diamond J (2005) Collapse: how societies choose to fail or survive. Penguin Books, London
15. H Dingle 2004 The Australo-Papuan bird migration system: another consequence of Wallace's Line Emu 104 95 108
16. AJ Drummond A Rambaut 2007 BEAST: Bayesian evolutionary analysis by sampling trees BMC Evol Biol 7 214
17. V Eastop 1966 A taxonomic study of Australian Aphidoidea (Homoptera) Aust J Zool 14 399 592
18. Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005) Virus taxonomy: classification and nomenclature of viruses. 8th report of the international committee on the taxonomy of viruses. Elsevier, New York
19. ME Ferguson PJ Bramel S Chandra 2004 Gene diversity botanical varieties in peanut (Arachis hypogaea L.) Crop Sci 44 1847 1854
20. M Fourment MJ Gibbs 2006 PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change BMC Evol Biol 6 1
21. Galloway R, Kemp E (1984) Late Cainozoic environments in Australia. In: Calaby J, Williams R (eds) Vertebrate zoogeography and evolution in Australasia. Hesperian Press, Marrickville, pp 82-95
22. AJ Gibbs AM Mackenzie K-J Wei MJ Gibbs 2008 The potyviruses of Australia Arch Virol 153 1411 1420 10.1007/s00705-008-0134-6
23. AJ Gibbs K Ohshima MJ Phillips MJ Gibbs 2008 The prehistory of Potyviruses: their initial radiation was during the dawn of agriculture PLoS ONE 3 e2523 10.1371/journal.pone.0002523
24. RG Gillespie EM Claridge SL Goodacre 2008 Biogeography of the fauna of French Polynesia: diversification within and between a series of hot spot archipelagos Philos Trans R Soc B 363 3335 3346
25. S Guindon O Gascuel 2003 PhyML-A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 52 696 704
26. C Ha P Revill RM Harding M Vu JL Dale 2008 Identification and sequence analysis of potyviruses infecting crops in Vietnam Arch Virol 153 45 60
27. TA Hall 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acid Symp Ser 41 95 98
28. JG Hather 1992 The archaeobotany of subsistence in the Pacific World Archaeol 24 70 81
29. Horridge A (2008) Origins and relationships of Pacific canoes and Rigs. In: Damon F, Mondragon C, Pearthree E, Di Piazza A (eds) Discovers of the Southern Sea. Oceanic Canoes across time and space. Archaeopress, Oxford
30. FMA Islam KE Basford RJ Redden AV Gonzalez PM Kroonenberg S Beebe 2002 Genetic variability in cultivated common bean beyond the two major gene pools Genet Resour Crop Evol 49 271 283
31. F Jeanmougin JD Thompson TJ Gibson M Gouy DG Higgins 1998 Multiple sequence alignment with Clustal X Trends Biochem Sci 23 403 405
32. Kennedy JS, Day MF, Eastop VF (1962) A conspectus of aphids as vectors of plant viruses. Commonwealth Institute of Entomology, London
33. AP Kershaw 1995 Environmental change in Greater Australia Antiquity 69 656 675
34. C Lanave G Preparata C Saccone G Serio 1984 A new method for calculating evolutionary substitution rates J Mol Evol 20 86 93
35. G Larson T Cucchi M Fujita E Matisoo-Smith J Robins A Anderson B Rolett M Spriggs G Dolman T-H Kim TD Thuy E Randi M Doherty D R.A R Bollt T Djubiantono B Griffin M Intoh E Keane P Kirch K-T Li M Morwood LM Pedriña PJ Piper RJ Rabett P Shooter G Van den Bergh E West S Wickler J Yuan A Cooper K Dobney 2007 Phylogeny and ancient DNA of Sus provides insights into Neolithic expansion in Island Southeast Asia and Oceania Proc Natl Acad Sci USA 104 4834 4839
36. JJ López-Moya RY Wang TP Pirone 1999 Context of the coat protein DAG motif affects potyvirus transmissibility by aphids J Gen Virol 80 3281 3288
37. Low T (2001) Feral future. The untold future of Australia's exotic invaders. Penguin Books, Australia
38. MacNight CC (1976) The voyage to Marege. Melbourne University Press, Melbourne
39. DP Martin C Williamson D Posada 2005 RDP2: recombination detection and analysis from sequence alignments Bioinformatics 21 260 262
40. Michael PW (1994) Alien plants. In: Groves RH (ed) Australian vegetation, 2nd edn. Cambridge University Press, Cambridge, pp 57-83
41. S Nebel 2007 Differential migration of shorebirds in the East Asian-Australasian Flyway Emu 107 14 18
42. Nix HA, Kalma JD (1972) Climate as a dominant control in the biogeography of Northern Australia and New Guinea. In: Walker D (ed) Bridge and barrier: the natural and cultural history of the Torres Strait. Australian National University, Canberra, pp 61-91
43. Pizzey G, Knight F (2007) The field guide to the birds of Australia, 8th edn. Harper Collins, Sydney
44. D Posada KA Crandall 1998 MODELTEST: testing the model of DNA substitution Bioinformatics 14 817 818
45. Purseglove JW (1966) Tropical crops: dicotyledons. Longman, England
46. N Saitou M Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol Biol Evol 4 406 425
47. P Savolainen YP Zhang J Luo J Lundeberg T Leitner 2002 Genetic evidence for an East Asian origin of domestic dogs Science 298 1610 1613
48. P Savolainen T Leitner AN Wilton E Matisoo-Smith J Lundeberg 2004 A detailed picture of the origin of the Australian dingo, obtained from the study of mitochondrial DNA Proc Natl Acad Sci USA 101 12387 12390
49. Shukla DD, Ward CW, Brunt AA (1994) The Potyviridae. CAB International, Wallingford
50. HE Simmons EC Holmes AG Stephenson 2008 Rapid evolutionary dynamics of zucchini yellow mosaic virus J Gen Virol 89 1081 1085
51. AK Singh J Smartt 1998 The genome donors of the groundnut/peanut (Arachis hypogaea L.) revisited J Genet Resour Crop Evol 45 113 116
52. AA Storey JM Ramírez D Quiroz DV Burley DJ Addison R Walter AJ Anderson TL Hunt JS Athens L Huynen EA Matisoo-Smith 2007 Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile Proc Natl Acad Sci USA 104 10335 10339
53. Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer Associates, Massachusetts
54. AR Templeton 2004 Statistical phylogeography: methods of evaluating and minimizing inference errors Mol Ecol 13 789 809 10.1046/j.1365-294X.2003.02041.x
55. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins 1997 The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 24 4876 4882
56. CD Von Dohlen DAJ Teulon 2003 Phylogeny and historical biogeography of New Zealand indigenous Aphidini aphids (Hemiptera, Aphididae); an hypothesis Ann Entomol Soc Am 96 107 116
57. CG Webster BA Coutts RAC Jones MGK Jones SJ Wylie 2007 Virus impact at the ancient ecosystem-recent agroecosystem interface: studies on three legume-infecting potyviruses in the Southwest Australian Floristic Region Plant Pathol 56 729 742
58. GF Weiller 1998 Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences Mol Biol Evol 15 326 335
59. S Wongkaew M Dollett 1990 Comparison of peanut stripe virus isolates using symptomatology on particular hosts abd serology Oleagineux 45 267 278
60. Z Yang 1994 Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods J Mol Evol 39 306 314
61. MF Zhao J Chen HY Zheng MJ Adams JP Chen 2003 Molecular analysis of Zucchini yellow mosaic virus isolates from Hangzhou, China J Phytopathol 151 307 311