Bioinformatics Vol. 16 no. 7 2000
Pages 573-582
© 2000 Oxford University Press
Original Paper |
Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences
1 Research School of Biological Sciences, The Australian National University, GPO Box 475, Canberra ACT 2601, Australia
Received on January 13, 2000
; revised on March 9, 2000
; accepted on March 14, 2000
Motivation: To devise a method that, unlike available methods, directly measures variations in phylogenetic signals in gene sequences that result from recombination, tests the significance of the signal variations and distinguishes misleading signals.
Results: We have developed a method, that we call
‘sister-scanning’, for assessing phylogenetic and
compositional signals in the various patterns of identity that occur
between four nucleotide sequences. A Monte Carlo randomization is
done for all columns (positions) within a window and 
-scores
are obtained for four real sequences or three real sequences with an
outlier that is also randomized. The usefulness of the approach is
demonstrated using tobamovirus and luteovirus sequences.
Contradictory phylogenetic signals were distinguished in both
datasets, as were regions of sequence that contained no clear signal
or potentially misleading signals related to compositional
similarities. In the tobamovirus dataset, contradictory phylogenetic
signals were separated by coding sequences up to a kilobase long
that contained no clear signal. Our re-analysis of this dataset
using sister-scanning also yielded the first evidence known to us of
an inter-species recombination site within a viral RNA-dependent RNA
polymerase gene together with evidence of an unusual pattern of
conservation in the three codon positions.
Availability: A program package, SiScan, for use under MS-DOS can be downloaded from http://life.anu.edu.au/with test data and instructions.
Contact: mgibbs{at}rsbs.anu.edu.au; johna{at}rsbs.anu.edu.au; gibbs{at}rsbs.anu.edu.au
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Varsani, D. N. Shepherd, A. L. Monjane, B. E. Owor, J. B. Erdmann, E. P. Rybicki, M. Peterschmitt, R. W. Briddon, P. G. Markham, S. Oluwafemi, et al. Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen J. Gen. Virol., September 1, 2008; 89(9): 2063 - 2074. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. M. Codoner and S. F. Elena The promiscuous evolutionary history of the family Bromoviridae J. Gen. Virol., July 1, 2008; 89(7): 1739 - 1747. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. T. Edwards, N. K. Fry, and T. G. Harrison Clonal population structure of Legionella pneumophila inferred from allelic profiling Microbiology, March 1, 2008; 154(3): 852 - 864. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Cardazzo, E. Negrisolo, L. Carraro, L. Alberghini, T. Patarnello, and V. Giaccone Multiple-Locus Sequence Typing and Analysis of Toxin Genes in Bacillus cereus Food-Borne Isolates Appl. Envir. Microbiol., February 1, 2008; 74(3): 850 - 860. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Ha, S. Coombs, P. Revill, R. Harding, M. Vu, and J. Dale Molecular characterization of begomoviruses and DNA satellites from Vietnam: additional evidence that the New World geminiviruses were present in the Old World prior to continental separation J. Gen. Virol., January 1, 2008; 89(1): 312 - 326. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Lefeuvre, D. P. Martin, M. Hoareau, F. Naze, H. Delatte, M. Thierry, A. Varsani, N. Becker, B. Reynaud, and J.-M. Lett Begomovirus 'melting pot' in the south-west Indian Ocean islands: molecular diversity and evolution through recombination J. Gen. Virol., December 1, 2007; 88(12): 3458 - 3468. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. E. Owor, D. P. Martin, D. N. Shepherd, R. Edema, A. L. Monjane, E. P. Rybicki, J. A. Thomson, and A. Varsani Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant J. Gen. Virol., November 1, 2007; 88(11): 3154 - 3165. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. W. Douhan, K. L. Huryn, and L. I. Douhan Significant diversity and potential problems associated with inferring population structure within the Cenococcum geophilum species complex. Mycologia, November 1, 2007; 99(6): 812 - 819. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. B. Thackray, C. E. Wobus, K. A. Chachu, B. Liu, E. R. Alegre, K. S. Henderson, S. T. Kelley, and H. W. Virgin IV Murine Noroviruses Comprising a Single Genogroup Exhibit Biological Diversity despite Limited Sequence Divergence J. Virol., October 1, 2007; 81(19): 10460 - 10473. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. M. Barr, S. R. Keller, P. K. Ingvarsson, D. B. Sloan, and D. R. Taylor Variation in Mutation Rate and Polymorphism Among Mitochondrial Genes of Silene vulgaris Mol. Biol. Evol., August 1, 2007; 24(8): 1783 - 1791. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. F. Boni, D. Posada, and M. W. Feldman An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets Genetics, June 1, 2007; 176(2): 1035 - 1047. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. J. Evans Ancestry Influences the Fate of Duplicated Genes Millions of Years After Polyploidization of Clawed Frogs (Xenopus) Genetics, June 1, 2007; 176(2): 1119 - 1130. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Ohshima, Y. Tomitaka, J. T. Wood, Y. Minematsu, H. Kajiyama, K. Tomimura, and A. J. Gibbs Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination J. Gen. Virol., January 1, 2007; 88(1): 298 - 315. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Heath, E. van der Walt, A. Varsani, and D. P. Martin Recombination Patterns in Aphthoviruses Mirror Those Found in Other Picornaviruses J. Virol., December 1, 2006; 80(23): 11827 - 11832. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Burzynski, M. Zbawicka, D. O. F. Skibinski, and R. Wenne Doubly Uniparental Inheritance Is Associated With High Polymorphism for Rearranged and Recombinant Control Region Haplotypes in Baltic Mytilus trossulus Genetics, November 1, 2006; 174(3): 1081 - 1094. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Varsani, E. van der Walt, L. Heath, E. P. Rybicki, A. L. Williamson, and D. P. Martin Evidence of ancient papillomavirus recombination J. Gen. Virol., September 1, 2006; 87(9): 2527 - 2531. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. W. Brunelle and G. F. Sensabaugh The ompA Gene in Chlamydia trachomatis Differs in Phylogeny and Rate of Evolution from Other Regions of the Genome Infect. Immun., January 1, 2006; 74(1): 578 - 585. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Delatte, D. P. Martin, F. Naze, R. Goldbach, B. Reynaud, M. Peterschmitt, and J.-M. Lett South West Indian Ocean islands tomato begomovirus populations represent a new major monopartite begomovirus group J. Gen. Virol., May 1, 2005; 86(5): 1533 - 1542. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. J. Evans, D. B. Kelley, D. J. Melnick, and D. C. Cannatella Evolution of RAG-1 in Polyploid Clawed Frogs Mol. Biol. Evol., May 1, 2005; 22(5): 1193 - 1207. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Tsaousis, D. P. Martin, E. D. Ladoukakis, D. Posada, and E. Zouros Widespread Recombination in Published Animal mtDNA Sequences Mol. Biol. Evol., April 1, 2005; 22(4): 925 - 933. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. P. Martin, C. Williamson, and D. Posada RDP2: recombination detection and analysis from sequence alignments Bioinformatics, January 15, 2005; 21(2): 260 - 262. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Tan, Y. Wada, J. Chen, and K. Ohshima Inter- and intralineage recombinants are common in natural populations of Turnip mosaic virus J. Gen. Virol., September 1, 2004; 85(9): 2683 - 2696. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Vigne, M. Bergdoll, S. Guyader, and M. Fuchs Population structure and genetic variability within isolates of Grapevine fanleaf virus from a naturally infected vineyard in France: evidence for mixed infection and recombination J. Gen. Virol., August 1, 2004; 85(8): 2435 - 2445. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. F. Bateson, R. E. Lines, P. Revill, W. Chaleeprom, C. V. Ha, A. J. Gibbs, and J. L. Dale On the evolution and molecular epidemiology of the potyvirus Papaya ringspot virus J. Gen. Virol., October 1, 2002; 83(10): 2575 - 2585. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Ohshima, Y. Yamaguchi, R. Hirota, T. Hamamoto, K. Tomimura, Z. Tan, T. Sano, F. Azuhata, J. A. Walsh, J. Fletcher, et al. Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread J. Gen. Virol., June 1, 2002; 83(6): 1511 - 1521. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. L. Domier, N. K. McCoppin, R. C. Larsen, and C. J. D'Arcy Nucleotide sequence shows that Bean leafroll virus has a Luteovirus-like genome organization J. Gen. Virol., June 1, 2002; 83(7): 1791 - 1798. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Guyader and D. G. Ducray Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products J. Gen. Virol., June 1, 2002; 83(7): 1799 - 1807. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Worobey, A. Rambaut, O. G. Pybus, D. L. Robertson, M. J. Gibbs, J. S. Armstrong, and A. J. Gibbs Questioning the Evidence for Genetic Recombination in the 1918 "Spanish Flu" Virus Science, April 12, 2002; 296(5566): 211a - 211a. [Full Text] [PDF]
|
|
|
|
|
|
M. J. Gibbs, J. S. Armstrong, and A. J. Gibbs Recombination in the Hemagglutinin Gene of the 1918 ""Spanish Flu"" Science, September 7, 2001; 293(5536): 1842 - 1845. [Abstract] [Full Text] [PDF]
|
|