Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions

Prokaryotic organisms share genetic material across species boundaries by means of a process known as horizontal gene transfer (HGT). This process has great significance for understanding prokaryotic genome diversification and unraveling their complexities. Phylogeny-based detection of HGT is one of the most commonly used methods for this task, and is based on the fundamental fact that HGT may cause gene trees to disagree with one another, as well as with the species phylogeny. Using these methods, we can compare gene and species trees, and infer a set of HGT events to reconcile the differences among these trees. In this paper, we address three factors that confound the detection of the true HGT events, including the donors and recipients of horizontally transferred genes. First, we study experimentally the effects of error in the estimated gene trees (statistical error) on the accuracy of inferred HGT events. Our results indicate that statistical error leads to overestimation of th...

• Type: Journal
• Year: 2007
• Where: JCB
• Authors: Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh
• Keywords: Gene Trees, HGT Events, Horizontal Gene Transfer, JCB 2007