Horizontal Gene Transfer Inference: Gene Presence-Absence Outperforms Gene Trees.

ABSTRACT: Horizontal gene transfer is a fundamental driver of prokaryotic evolution, facilitating the acquisition of novel traits and adaptation to new environments. Despite its importance, methods for inferring horizontal gene transfer are rarely systematically compared, leaving a gap in our understanding of their relative strengths and limitations. Validating horizontal gene transfer inference methods is challenging due to the absence of a genomic fossil record that could confirm historical transfer events. Without an empirical gold standard, new inference methods are typically validated using simulated data; however, these simulations may not accurately capture biological complexity and often embed the same assumptions used in the inference methods themselves. Here, we leverage the tendency of ho

SUBMITTER: Mishra S 

PROVIDER: S-EPMC12301182 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature