Microbial evolutionary reconstruction in the presence of mosaic sequences

Abstract

Phylogenetic reconstruction is central to many research areas in biology, from evolutionary biology to genomic epidemiology. Reconstruction of a phylogeny is often done based on comparative analysis of gene or protein sequences, or even whole genome sequences. Recombination and horizontal gene transfer (HGT), however, complicate this task, violating the very basic and common assumption in the standard molecular phylogenetic analysis, that is, all positions in the molecular sequences analyzed share the same underlying evolutionary history. This issue is most problematic in microbial evolutionary studies, where recombination and HGT are pervasive. This chapter begins with an overview of recombination and HGT in viruses and bacteria and guides the reader through the process of how to detect potential recombination and HGT among molecular sequences. The impacts of mixed evolutionary signals on standard phylogenetic reconstruction are discussed, and various strategies of how to deal with this problem in evolutionary reconstruction are outlined.