A novel exploratory method for visual recombination detection

Abstract

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.

Figure 1

Highway and occupancy plots for simulated data with no recombination.

Figure 2

Highway and occupancy plots for simulated data with recombination and balanced trees.

Figure 3

Highway and occupancy plots for simulated data with recombination and unbalanced trees.

Figure 4

Highway and occupancy plots for an HIV-1 gag region alignment containing the recombinant sequence 93BR029. The red vertical lines indicate the two putative breakpoints.

Figure 5

Highway and occupancy plots for the 1918 influenza virus dataset. The window size varies from 400 to 800 bp.

Figure 6

Bootscan plots. (a) HIV-1 data; (b) 1918 influenza virus data.

Figure 7

The quartet-mapping triangle. (a) Barycentric coordinate system; (b) polar representation. In both (a) and (b), C denotes the centroid (1/3, 1/3, 1/3) and P some general point (s₁, s₂, s₃).