| [1] | Shearer PL, Bonne N, Clark P, Sharp M, Raidal SR (2008) Beak and feather disease virus infection in cockatiels (Nymphicus hollandicus). Avian Pathol 37: 75–81.
|
| [2] | Pass DA, Perry RA (1984) The pathology of psittacine beak and feather disease. Aust Vet J 61: 69–74.
|
| [3] | Ritchie B, Niagro F, Latimer K, Lukert P, WL S, et al. (1990) Ultrastructural, protein composition, and antigenic comparison of psittacine beak and feather disease virus purified from four genera of psittacine birds. J Wildl Dis 26: 196–203.
|
| [4] | Ritchie BW, Niagro FD, Lukert PD, Steffens Iii WL, Latimer KS (1989) Characterization of a new virus from cockatoos with psittacine beak and feather disease. Virology 171: 83–88.
|
| [5] | Raidal SR, McElnea CL, Cross GM (1993) Seroprevalence of psittacine beak and feather disease in wild psittacine birds in New South Wales. Aust Vet J 70: 137–139.
|
| [6] | Latimer KS, Rakich PM, Kircher IM, Ritchie BW, Niagro FD, et al. (1990) Extracutaneous Viral Inclusions in Psittacine Beak and Feather Disease. J Vet Diagn Invest 2: 204–207.
|
| [7] | Ritchie BW (1995) Circoviridae. Avian viruses, function and control. Wingers Publishing Inc, Lake Worth, 223–252.
|
| [8] | Perry RA (1981) A Psittacine Combined Beak and Feather Disease Syndrome with particular reference to the Australian Cockatoos Cacatua galerita (Sulphur crested cockatoo), Cacatua leadbeateri (Major Mitchell or Pink Cockatoo), Cacatua roseicapella (Galah or Rose breasted Cockatoo) and Cacatua sanguinea (Little Corella), In Proceedings No. 55 Refresher Course on Aviary and Caged Birds. 81–108. The Post-graduate Committee in Veterinary Science, Mosman, Australia.
|
| [9] | Heath L, Martin DP, Warburton L, Perrin M, Horsfield W, et al. (2004) Evidence of Unique Genotypes of Beak and Feather Disease Virus in Southern Africa. J Virol 78: 9277–9284.
|
| [10] | Kondiah K, Albertyn J, Bragg RR (2006) Genetic diversity of the Rep gene of beak and feather disease virus in South Africa. Arch Virol 151: 2539–2545.
|
| [11] | Mankertz A, Mankertz J, Wolf K, Buhk HJ (1998) Identification of a protein essential for replication of porcine circovirus. J Gen Virol 79: 381–384.
|
| [12] | Niagro FD, Forsthoefe lAN, Lawther RP, Kamalanathan L, Ritchie BWL, K.S., et al (1998) Beak and feather disease virus and porcine circovirus genomes: intermediates between the geminiviruses and plant circoviruses. Arch of Virololy 143: 1723–1744.
|
| [13] | Julian L, Piasecki T, Chrz？stek K, Walters M, Muhire B, et al. (2013) Extensive recombination detected amongst Beak and feather disease virus isolates from breeding facilities in Poland. J Gen Virol 94: 1086–1095.
|
| [14] | Duffy S, Holmes EC (2008) Phylogenetic Evidence for Rapid Rates of Molecular Evolution in the Single-Stranded DNA Begomovirus Tomato Yellow Leaf Curl Virus. J Virol 82: 957–965.
|
| [15] | Bassami MRYI, Berryman D, Wilcox GE, Raidal SR (2001) Genetic Diversity of Beak and Feather Disease Virus Detected in Psittacine Species in Australia. Virology 279: 392–400.
|
| [16] | Varsani A, Regnard GL, Bragg R, Hitzeroth II, Rybicki EP (2011) Global genetic diversity and geographical and host-species distribution of beak and feather disease virus isolates. J Gen Virol 92: 752–767.
|
| [17] | Higgins PJe (1999) Handbook of Australian, New Zealand and Antarctic Birds. Volume 4: Parrots to Dollarbird. Oxford University Press, Melbourne.
|
| [18] | IUCN (2013) IUCN Red List of Threatened Species. Version 2013.1. Available: http://www.iucnredlist.org/details/10600？1485/0. Accessed 14 August 2013.
|
| [19] | Pritchard R (2012) Update on the Orange-bellied Parrot Recovery Program.
|
| [20] | Brown PB (1988) A captive breeding program for Orange-bellied Parrots. Australian Aviculture 42: 165–175.
|
| [21] | Harris J (2006) Pathology, diagnostics, implications and strategies in a breeding colony of Orange-bellied Parrots (Neophema chrysogaster). In Proceedings: Australian Committee Association of Avian Veterinarians. G. Cross, (ed). Wellington, New Zealand, 143–145.
|
| [22] | Peters A, Patterson EI, Baker GBB, Holdsworth M, Sarker S, et al. (2013) Evidence of psittacine beak and feather disease virus (BFDV) spillover into wild critically endangered orange-bellied parrots (Neophema chrysogaster). J Wildl Dis (Accepted).
|
| [23] | Khalesi B, Bonne N, Stewart M, Sharp M, Raidal S (2005) A comparison of haemagglutination, haemagglutination inhibition and PCR for the detection of psittacine beak and feather disease virus infection and a comparison of isolates obtained from loriids. J Gen Virol 86: 3039–3046.
|
| [24] | Ypelaar I, Bassami MR, Wilcox GE, Raidal SR (1999) A universal polymerase chain reaction for the detection of psittacine beak and feather disease virus. Vet Microbiol 68: 141–148.
|
| [25] | Bonne N, Clark P, Shearer P, Raidal S (2008) Elimination of False-Positive Polymerase Chain Reaction Results Resulting from Hole Punch Carryover Contamination. J Vet Diagn Invest 20: 60–63.
|
| [26] | Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680.
|
| [27] | Drummond AJ, Suchard MA, Xie D, Rambaut A (2012) Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29: 1969–1973.
|
| [28] | Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences. Mol Biol Evol 22: 1185–1192.
|
| [29] | Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Meth 9: 772–772.
|
| [30] | Andrew R (2009) FigTree v1.4 Computer Program and Documentation Distributed by the Author. Avaailable: http://tree.bio.ed.ac.uk/software/figtre？e/.
|
| [31] | Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SDW (2006) Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm. Mol Biol Evol 23: 1891–1901.
|
| [32] | Delport W, Poon AFY, Frost SDW, Pond SLK (2010) Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26: 2455–2457.
|
| [33] | Suchard M, Weiss R, Dorman K, Sinsheimer J (2003) Inferring spatial phylogenetic variation along nucleotide sequences: a multiple change-point model. Journal of the American Statistical Assocation 98: 427–437.
|
| [34] | Minin V, Dorman K, Fang F, Suchard M (2005) Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics 21: 3034–3042.
|
| [35] | Padidam M, Sawyer S, Fauquet CM (1999) Possible Emergence of New Geminiviruses by Frequent Recombination. Virology 265: 218–225.
|
| [36] | Martin DP, Posada D, Crandall KA, Williamson C (2005) A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21: 98–102.
|
| [37] | Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proc Natl Acad Sci U S A 98: 13757–13762.
|
| [38] | Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573–582.
|
| [39] | Martin D, Rybicki E (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16: 562–563.
|
| [40] | Martin DP, Lemey P, Lott M, Moulton V, Posada D, et al. (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26: 2462–2463.
|
| [41] | Murrell B, Moola S, Mabona A, Weighill T, Sheward D, et al. (2013) FUBAR : A Fast, Unconstrained Bayesian AppRoximation for inferring selection. Mol Biol Evol 30: 1196–1205.
|
| [42] | Kosakovsky Pond SL, Frost SDW (2005) Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection. Mol Biol Evol 22: 1208–1222.
|
| [43] | Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, et al. (2012) Detecting Individual Sites Subject to Episodic Diversifying Selection. PLoS Genet 8: e1002764.
|
| [44] | Poon AFY, Lewis FI, Pond SLK, Frost SDW (2007) An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope. PLoS Comput Biol 3: e231.
|
| [45] | Ilyina TV, Koonin EV (1992) Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res 20: 3279–3285.
|
| [46] | Laura AS, Andrew R, Oliver GP, Edward CH (2006) JC Virus Evolution and Its Association with Human Populations. J Virol: 9928–9933.
|
| [47] | Hatwell JN, Sharp PM (2000) Evolution of human polyomavirus JC. J Gen Virol 81: 1191–1200.
|
| [48] | Kundu S, Faulkes CG, Greenwood AG, Jones CG, Kaiser P, et al. (2012) Tracking Viral Evolution during a Disease Outbreak: the Rapid and Complete Selective Sweep of a Circovirus in the Endangered Echo Parakeet. J Virol 86: 5221–5229.
|
| [49] | Todd D (2000) Circoviruses: Immunosuppressive threats to avian species: A review. Avian Pathol 29: 373–394.
|
| [50] | Rahaus M, Desloges N, Probst S, Loebbert B, Lantermann W, et al. (2008) Detection of beak and feather disease virus DNA in embryonated eggs of psittacine birds. Veterinarni Medicina 53: 53–58.
|
| [51] | Todd D (2004) Avian circovirus diseases: lessons for the study of PMWS. Vet Microbiol 98: 169–174.
|
| [52] | Gerlach H (1994) CCircoviridae-psittacine beak and feather disease virus, p 894–903. In Ritchie BW, Harrison GT, Harrison LR (ed), Avian medicine: principles and practice. Wingers Publishing, Inc, Lake Worth, FL.
|
| [53] | Nozawa M, Suzuki Y, Nei M (2009) Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci U S A 106: 6700–6705.
|
| [54] | Anisimova M, Bielawski JP, Yang Z (2002) Accuracy and Power of Bayes Prediction of Amino Acid Sites Under Positive Selection. Mol Biol Evol 19: 950–958.
|
| [55] | Duffy S, Shackelton LA, Holmes EC (2008) Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 9: 267–276.
|
| [56] | Ng TFF, Manire C, Borrowman K, Langer T, Ehrhart L, et al. (2009) Discovery of a Novel Single-Stranded DNA Virus from a Sea Turtle Fibropapilloma by Using Viral Metagenomics. J Virol 83: 2500–2509.
|
| [57] | Andersson M, Scherman K, L R (2013) Multiple-strain infections of Borrelia afzelii: a role for within-host interactions in the maintenance of antigenic diversity? The American Naturalist 181: 545–554.
|
| [58] | Lord CC, Barnard B, Day K, Hargrove JW, McNamara JJ, et al. (1999) Aggregation and distribution of strains in microparasites. Philos Trans R Soc Lond B Biol Sci. 354: 799–807.
|
| [59] | Alizon S, de Roode JC, Michalakis Y (2013) Multiple infections and the evolution of virulence. Ecol Lett 16: 556–567.
|
| [60] | Walsh PS, Erlich HA, Higuchi R (1992) Preferential PCR amplification of alleles: mechanisms and solutions. Genome Res 1: 241–250.
|
| [61] | Perales C, Agudo R, Domingo E (2009) Counteracting Quasispecies Adaptability: Extinction of a Ribavirin-Resistant Virus Mutant by an Alternative Mutagenic Treatment. PLoS ONE 4: e5554.
|
| [62] | Lauring AS, Andino R (2010) Quasispecies Theory and the Behavior of RNA Viruses. PLoS Pathog 6: e1001005.
|
| [63] | Grasland B, Loizel C, Blanchard P, Oger A, Nignol A-C, et al. (2005) Reproduction of PMWS in immunostimulated SPF piglets transfected with infectious cloned genomic DNA of type 2 porcine circovirus. Vet Res 36: 685–697.
|
| [64] | Shackelton LA, Holmes EC (2006) Phylogenetic Evidence for the Rapid Evolution of Human B19 Erythrovirus. J Virol 80: 3666–3669.
|
| [65] | Shackelton LA, Parrish CR, Truyen U, Holmes EC (2005) High rate of viral evolution associated with the emergence of carnivore parvovirus. Proc Natl Acad Sci U S A 102: 379–384.
|
| [66] | Linmei G, Jiangtao Z, Xueping Z, Hongye L (2007) Genetic Structure and Population Variability of Tomato Yellow Leaf Curl China Virus. J Virol 81: 5902–5907.
|
| [67] | Umemura T, Tanaka Y, Kiyosawa K, Alter HJ, Shih JW-K (2002) Observation of positive selection within hypervariable regions of a newly identified DNA virus (SEN virus). FEBS Lett 510: 171–174.
|
| [68] | Ramsden C, Melo FL, Figueiredo LM, Holmes EC, Zanotto PMA, et al. (2008) High Rates of Molecular Evolution in Hantaviruses. Mol Biol Evol 25: 1488–1492.
|
| [69] | Duffy S, Holmes EC (2009) Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J Gen Virol 90: 1539–1547.
|
| [70] | Worobey M, Holmes EC (1999) Evolutionary aspects of recombination in RNA viruses. J Gen Virol 80: 2535–2543.
|
| [71] | Awadalla P (2003) The evolutionary genomics of pathogen recombination. Nat Rev Genet 4: 50–60.
|
| [72] | Martin DP, Biagini P, Lefeuvre P, Golden M, Roumagnac P, et al. (2011) Recombination in Eukaryotic Single Stranded DNA Viruses. Viruses 3: 1699–1738.
|
| [73] | van der Walt E, Rybicki EP, Varsani A, Polston JE, Billharz R, et al. (2009) Rapid host adaptation by extensive recombination. J Gen Virol 90: 734–746.
|
| [74] | Khatchikian D, Orlich M, Rott R (1989) Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the haemagglutinin gene of an influenza virus. Nature 340: 156–157.
|
| [75] | Belyi VA, Levine AJ, Skalka AM (2010) Sequences from Ancestral Single-Stranded DNA Viruses in Vertebrate Genomes: the Parvoviridae and Circoviridae Are More than 40 to 50 Million Years Old. J Virol 84: 12458–12462.
|
| [76] | Lefeuvre P, Lett J-M, Varsani A, Martin DP (2009) Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses. J Virol 83: 2697–2707.
|
| [77] | Massaro M, Ortiz-Catedral L, Julian L, Galbraith J, Kurenbach B, et al. (2012) Molecular characterisation of beak and feather disease virus (BFDV) in New Zealand and its implications for managing an infectious disease. Arch Virol 157: 1651–1663.
|
| [78] | Robert S (1992) DNA Looping. Annu Rev Biochem 61: 199–223.
|
