Sliding MinPD

Building evolutionary networks of serial samples via a recombination detection approach

Patricia Buendia and Giri Narasimhan
Bioinformatics Research Group (BioRG)
Florida International University

Home |  Features |  Supplementary Material |  Source Code

Abstract

Traditional phylogenetic methods assume tree-like evolutionary models and are known to perform poorly when provided with sequence data from recombining, fast-evolving viruses. Furthermore, these methods assume that all the sequence data are from contemporaneous taxa, which is not valid for serially-sampled data. A more general approach is needed one that is mindful of the sampling times of the input sequences and that reconstructs the viral evolutionary relationships in the form of a network structure with implicit representations of recombination events. The underlying network organization may reveal unique patterns of viral evolution and could help explain the emergence of disease-associated mutants and drug-resistant strains, with implications for patient prognosis and treatment strategies. The method we developed, referred to as Sliding MinPD, reconstructs evolutionary networks of serially-sampled sequences by combining minimum pairwise distance measures with automated recombination detection based on a sliding window approach. The method, an improved version of the MinPD method [1], was tested using simulated data and was also applied to a set of serially-sampled HIV sequences from a single patient. The type of recombinant networks output by the Sliding MinPD method are referred to as serial evolutionary networks, and are a generalization of the evolutionary framework introduced by Holmes et al. in his 1992 study [2] .

 

[1]  Buendia, P. and Narasimhan, G. (2004). MinPD: Distance-based Phylogenetic Analysis and Recombination Detection of Serially-Sampled HIV Quasispecies. Proc. IEEE Comput. Sys. Bioinform. Conf., Stanford, CA 

[2] Holmes, E. C., Zhang, L. Q., Simmonds, P., Ludlam, C. A., and Brown, A. J. (1992). Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc. Natl. Acad. Sci. U. S. A.:4835-4839