Navigating Incongruence and Uncertainty in Genome-scale Phylogenetic and Ancestral State Reconstructions of Enterobacteria
A robust phylogenetic framework is a cornerstone of evolutionary analyses that illuminates myriad biological questions. Extensive horizontal gene transfer in some groups of bacteria can be a significant confounding factor in detection of a predominant phylogenetic history representing even the majority of a given set of genomes. Regions of the genomes or individual genes with alternate evolutionary histories can also provide biological insights. Taxon sampling biases and inherent data limitations for individual genes can make it challenging to distinguish between true incongruence and uncertainty. Here, we present comparative genomic analyses of enterobacteria, a ubiquitous model family with members free-living in soil, water and air, and associated with hosts as diverse as humans and potatoes. Through a combination of orthology prediction, gene-by-gene, total evidence, coalescent-based, and quartet-based approaches to phylogenetic reconstruction, coupled with inferences on ancestral genome content, metabolic and regulatory networks, we dissect the genome-wide evolutionary history of enterobacteria with the ultimate goal of understanding the emergence of complex traits such as host-range, pathogenicity and responses to abiotic environmental parameters like oxygen availability.