Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples

Abstract

Determining the evolutionary history of a sampled sequence can become quite complex when multiple recombination events are part of its past. With at least five new recombination detection methods published in the last year, the growing list of over 40 methods suggests that this field is generating a lot of interest. In previous studies comparing recombination detection methods, the evaluation procedures did not measure how many recombinant sequences, breakpoints and donors were correctly identified. In this paper we will present the algorithm RecIdentify that scans a phylogenetic network and uses its edge lengths and topology to identify the parental/donor sequences and breakpoint positions for each query sequence. RecIdentify findings can be used to evaluate the output of recombination detection programs. RecIdentify may also assist in understanding how network size and complexity may shape recombination signals in a set of DNA sequences. The results may prove useful in the phylogenetic study of serially-sampled viral data with recombination events.