A novel exploratory method for visual recombination detection

A versatile visual approach for detecting recombination and identifying recombination breakpoints within a sequence alignment is presented. The method is based on two novel diagrams - the highway plot and the occupancy plot - that graphically portray phylogenetic inhomogeneity along an alignment, and can be viewed as a synthesis of two widely used but unrelated methods: bootscanning and quartet-mapping. To illustrate the method, simulated data and HIV-1 and influenza A datasets are investigated.

[1]  M. Eigen,et al.  Statistical geometry in sequence space: a method of quantitative comparative sequence analysis. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[2]  M. Braga,et al.  Exploratory Data Analysis , 2018, Encyclopedia of Social Network Analysis and Mining. 2nd Ed..

[3]  S. Sawyer.  Statistical tests for detecting gene conversion. , 1989, Molecular biology and evolution.

[4]  J. Hein.  Reconstructing evolution of sequences subject to recombination using parsimony. , 1990, Mathematical biosciences.

[5]  Peter Brimblebecombe,et al.  Picture this , 1995, Nature.

[6]  D. Burke,et al.  Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. , 1995, AIDS research and human retroviruses.

[7]  E. Holmes,et al.  A likelihood method for the detection of selection and recombination using nucleotide sequences. , 1997, Molecular biology and evolution.

[8]  Andrew Rambaut,et al.  Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees , 1997, Comput. Appl. Biosci..

[9]  K. Strimmer,et al.  Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[10]  P. Sharp,et al.  A Comprehensive Panel of Near-Full-Length Clones and Reference Sequences for Non-Subtype B Isolates of Human Immunodeficiency Virus Type 1 , 1998, Journal of Virology.

[11]  K. Lole,et al.  Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination , 1999, Journal of Virology.

[12]  Edward J. Wegman.  Data Mining and Visualization : Some Strategies , 1999 .

[13]  Gráinne McGuire,et al.  A Bayesian Model for Detecting Past Recombination Events in DNA Multiple Alignments , 2000, J. Comput. Biol..

[14]  J. Hein,et al.  Consequences of recombination on traditional phylogenetic analysis. , 2000, Genetics.

[15]  J. Hein,et al.  Recombination and the molecular clock. , 2000, Molecular biology and evolution.

[16]  Mark J. Gibbs,et al.  Recombination in the Hemagglutinin Gene of the 1918 "Spanish Flu" , 2001, Science.

[17]  M. Worobey,et al.  A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria. , 2001, Molecular biology and evolution.

[18]  J. Hein,et al.  A simulation study of the reliability of recombination detection methods. , 2001, Molecular biology and evolution.

[19]  K. Crandall,et al.  Intraspecific gene genealogies: trees grafting into networks. , 2001, Trends in ecology & evolution.

[20]  K. Crandall,et al.  The Effect of Recombination on the Accuracy of Phylogeny Estimation , 2002, Journal of Molecular Evolution.

[21]  K. Crandall,et al.  Evaluation of methods for detecting recombination from DNA sequences: Computer simulations , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[22]  C. Brown,et al.  The power to detect recombination using the coalescent. , 2001, Molecular biology and evolution.

[23]  A. von Haeseler,et al.  Quartet-mapping, a generalization of the likelihood-mapping procedure. , 2001, Molecular biology and evolution.

[24]  Martin Vingron,et al.  TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing , 2002, Bioinform..

[25]  O. Pybus,et al.  Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus. , 2002, Science.

[26]  Philip Ball.  Data visualization: Picture this , 2002, Nature.

[27]  A. Dress,et al.  δ Plots: A Tool for Analyzing Phylogenetic Distance Data , 2002 .

[28]  D. Posada.  Evaluation of methods for detecting recombination from DNA sequences: empirical data. , 2002, Molecular biology and evolution.

[29]  Daniel H. Huson,et al.  VisRD--visual recombination detection , 2004, Bioinform..